ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgtttatgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG

Basic information

species	Zea mays
transcript	GRMZM2G178341_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 3

tagccgtggccttcaaattt-taaatttttgtatgctgcatgtcattgtttatgtagttcctaagttaacagt-cacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
     ||  ||     |||  | |  | ||| || |          |||| |   |  |  || | |  ||   | | |   | ||  |  |   | | ||||||||||||||||||| | |||||||||||||||||||| ||||| |||||||||||||| || || ||| | || || ||||| ||||| |||||||||
-gtttgttacccaggcattcatcatgtattggatccctttaacttatgttgac-catcttttacgctctcatcacccttgcgctcacttgttccttgtacagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTGCGTGGGCAGCACACCAAGACAACCGGAAGGAGGGGTAAGACTGTCGGTGTGTCCAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G36880.2 (Glycine max), 3'ss of exon 3

---tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgtttatgtagttcctaagttaacagtcac-atattcgcatct-tcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
    |   ||   | | |||   || |    | ||||  | |   ||| ||  |  || || |||  ||||     |  | |||   || | |  | |  ||||||||||| |||||| || | ||||||||||| || ||||| ||||||||||| ||||||||||||||  |  | || |||||||||||||| |||||||||
cttcatttgttttcataaaaacgtatagaaatatatg--gaaacacat-gtcaaattactttcta--ttaaatccaatgaaattgatatttatacttgcatgcagGAACCATCGTGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCCAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G08690.1 (Glycine max), 3'ss of exon 3

--tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgtttatgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
  |  | |   | |   |||      | |||||   ||   |    ||||  || |  ||    | | |||| | |||| ||    ||||  |  | ||||| || ||||||||| || | ||||||||||| || ||||| ||||| |||||||| ||||| |||||  |  | || ||||||||||||||||| ||||||
atttcctgctacttcttaatagggtctctttgtgccct-tgttaagttgtgcatattattaggtaat-aacactaacatcttgtattcttactattatgcagAAATCACCGTGGTTTGAGGCACTACTGGGGTCTTCGTGTTCGTGGTCAGCACACTAAGACTACTGGTCGCAGGGGTAAAACTGTTGGTGTCTCTAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G30970.1 (Glycine max), 3'ss of exon 3

-----tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgtttatgtagttcctaagttaacagtcacatattcgcatcttcttggtt-tgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
     |    || | | ||| |||||   | | ||     ||  || |  || |||   |  |  |  | |||    |  | | ||  |||       || ||||| |||||||||||| || | |||||||||||||| ||||||||||| |||||||||||||| |||||| |  | ||||| |||||||| ||||| ||||||
taaaattctggttgtcctcagatttt---tgtgtgggcattgtctgcc--tgattaaaaaaatattg-gctaatgagctgaaaatcatatccctactattatgcagAAACCACCGTGGTTTGAGGCACTACTGGGGCCTTCGTGTCCGTGGTCAGCACACCAAGACTACTGGCCGCAGGGGAAAGACTGTTGGGGTCTCTAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G36610.2 (Glycine max), 3'ss of exon 3

tagccgtggccttcaaattttaaatttttgtatgctgcatgt---cattgttta--tgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
      ||    | ||||  |   |      | ||    |||   ||||||||   || |   | |  | ||||   |  | |||     |||  |  | ||||| |||||||||||| || | || ||||||||||| ||||||||||| |||||||||||||| |||||| |  | ||||| |||||||||||||| ||||||
-----ttgttaataaaatccttgttgccctcaagcattgtgtatgcattgtttgattgaaaaacattggctaacgaactgaaattgtatccttactattatgcagAAACCACCGTGGTTTGAGGCATTACTGGGGCCTTCGTGTCCGTGGTCAGCACACCAAGACTACTGGCCGTAGGGGAAAGACTGTTGGTGTCTCTAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 3

-tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgtttatg--tagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
    | |   || |  |  | |  |  ||   ||  |  ||    ||||    |  ||   | | || |  ||  |  ||       | ||||||   ||||||||||| || ||| || | ||||||||||| || ||||| ||||||||||| ||||||||||||||  |  | || |||||||||||||| || ||||||
tcctctgcttccgttcatctatggaccttg--attttatattctgttgtcagagagtaaaacatgagattgcatccttattgatttttattcttg-catgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3

tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgttta----tgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
            | ||     |||       ||  | | | || ||||| |    || |      | | | | | |      |||   | |      |    || |||||||||||| || | || |||||||| ||||||||| | || || ||||||||||| |||||  |  | ||||| |||||||||||||| ||||||
-----------gtaaatacaaaaaccaacagataattcttatctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G22780.1 (Arabidopsis thaliana), 3'ss of exon 3

tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgtttatgtagttcctaagtta-acagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
 |    |  |      ||  |   ||| | | |  |   | | ||  |  || |||  | |   ||  || | |  | |||  ||   |  || |   ||| ||||| ||||||||| | ||||||||||| |||||||| ||||| ||||||||||| ||||| ||  | || ||||| ||||||||||| |||||||||
aatgatttactgatgcatcctttgtttctctcttgttgttctgataatcgatatagaactttgtttgtactgactgagattgtcactgtaatg-taaacagAAACCATCGTGGTCTGAGGCACTACTGGGGTCTCCGTGTACGTGGACAGCACACCAAAACCACCGGACGCCGTGGAAAGACTGTTGGTGTTTCCAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G34030.1 (Arabidopsis thaliana), 3'ss of exon 3

-tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgtttatgtagttcctaag----ttaacagtcacatattcgcatcttcttggtttg--cagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
 ||  |       |||  |||   ||  |  |       ||  |||  |  || |     ||| |    |||| | |      || |||| |||||    ||  ||| ||||| ||||||||| | || |||||||| |||||||| ||||| || ||||||||||| |||||  |  | ||||| ||||||||||| || ||||||
gtaaacccattagtca--tttctgatcctaat----catataacatgataaatatgtcctctaggggctttaataatggtggttttgcattttcttacaatgaacagAAACCATCGTGGTCTGAGACATTACTGGGGTCTCCGTGTTCGTGGACAACACACCAAGACAACTGGTCGCAGAGGAAAGACTGTTGGTGTGTCTAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 3

tagccgtggccttcaaattttaaatttttgtatgc-tgcatgtcattgtttatgt-agttcctaagttaacagtcacatattcgcatc-ttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
|   ||||  | |    |  | | |||   |     || ||     |||||||   || |  || |    |||| | | | |   ||| || |   |   |||||||||||||||||| || ||||||||||| || ||||| || || || ||||||||||| |||||| |  | || ||||||||||||||||| || |||
tgctcgtgagcattgcctacttattttcactgcatatgtatccatctgtttataagaggtgatagg--ggcagtta-acactgatatcattttcaatggacagGAACCACCGTGGTCTTCGACACTACTGGGGTCTACGTGTACGCGGACAACACACCAAGACAACTGGCCGCAGAGGGAAAACTGTTGGTGTCTCAAAAAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0072g00060.t01 (Vitis vinifera), 3'ss of exon 4

tagccgtggccttcaaattttaaatttttgtatgctgcatgtcatt--gtttatgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
  | |   |  | ||   |||    |  |   |  || |||   ||  |  || || |     ||  | | | |  ||  |   | |  |  || | ||||||||||||||||||||| | |||||||||||||||||||| || |||||||||||||||||||| ||  |  | ||||| |||||||||||||| ||||||
agggcaccgtgtccattgtttgtggtagtaggttgtgaatgaagtttaggctaggtgggga--aacatgatactttcagctaatcttgatactgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCACACCAAGACCACAGGTCGTAGAGGAAAGACTGTTGGTGTCTCTAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S14_438V6.1 (Physcomitrella patens), 3'ss of exon 3

-tagccgtggccttcaaattttaaatttttgtatgct----gcatgtcattgtttatgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
   |     |      |||| | | |  |   ||| |    |  || ||||  ||  |  ||   | | || ||  |  |  |    ||| |  || ||| |||||||||||||||| || || |||||||||||| | || || ||||| ||||| |||||||| || ||  | || |||| ||| || ||||| |||||||||
tctgagacagttcctcaattgttagtgatcacatgtttttagtttgccatt-cttgggcggtgtttta-ttgactctttctgaa--acatttaatttgtt-gcagGAACCACCGTGGACTTCGACACTACTGGGGCTTGCGCGTGCGTGGACAGCATACCAAGACTACAGGGCGACGTGGAAGAACCGTCGGTGTGTCCAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S72_222V6.2 (Physcomitrella patens), 3'ss of exon 3

tagcc--gtggccttcaaattt--taaatttttgtatgctgcatgtcattg-tttatgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
||| |   |   |||| |      | ||   | |     | ||| |    | ||| ||| |||| |    | | ||    | | | |    |  ||| ||  |||||| ||||||||||| ||||| ||||||||| | || || ||||| || ||||||||||| || ||  | || |||| ||| |||||||| |||||||||
tagtctcattttcttcgagcgcaatgaaggctcgggcttttcatatttgcgatttttgtggttcttc--ctgataggt-tagagttgatgttgattgatt--cagGAATCACCGTGGTCTTCGTCATTACTGGGGCTTGCGCGTGCGTGGTCAACACACCAAGACTACCGGACGACGTGGAAGAACCGTTGGTGTGTCCAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S242_94V6.1 (Physcomitrella patens), 3'ss of exon 3

tagccgtggccttcaaattttaaatttttgtatgctgcatgt-cattgtttatgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
  |  ||    ||   ||  |     |||  | | ||   || | |||   || | |||      |  || |       |   |     ||    ||||||||||||||||||||| ||||||||||||||| | || || || || |||||||| ||||| |||||  |||| ||||  || || ||||| |||||||||
-gggtgtcttgtttgtatcatcccggtttacaggttgtcggttctttgaagatctggttttgttttctactgattggagtcgactgtggctattattgcagGAACCACCGTGGTCTTCGTCACTACTGGGGCTTGCGAGTACGCGGACAGCACACAAAGACTACTGGACGGCGTGGAAGGACCGTCGGTGTGTCCAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S215_71V6.1 (Physcomitrella patens), 3'ss of exon 3

---------------------------------------------------tagccgtggccttcaa--attttaaatttttg-tatgctgcatgtcattgt-ttatgtagttcctaagttaacagtcacatattcgcatctt-----cttggtttg-------cagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
                                                   ||          |  |  | ||   ||||    ||||| |||    ||||  ||  |     | | ||  |    | |     | |  || |     |||||||||       |||||||||||||||||| ||||||||||||||| | || || ||||| || ||||| ||||| |||||  | || ||||  || || ||||| || ||||||
gttagtgaaattttcttcttccagtttatgattaatgcttattcaaatttatatttacaaatatagatcacttgtgatttgaactatgcagcactctattgcattgcgcctggctttaggcagtgctgattgccttgtgtcatgacggcttggtttgggggatgcagGAACCACCGTGGTCTTCGTCACTACTGGGGCTTGCGAGTACGTGGTCAACACACGAAGACAACTGGACGTCGTGGAAGGACCGTCGGTGTGTCTAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 3

tagccgtggccttcaaattt--taaatttttgtatgctgcatgtcattgtttatgtagttcctaagttaacagtcacatattcgcatcttcttggtt-tgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
    | |||   | |||| |  || || ||| || ||| |   ||||    |||||     | |   |     |     |   ||    |  || |  |||||||||||||||||||| ||||||||||||||| | ||||| ||||| || ||||||||||| ||||| || || || | ||| || || || |||||||||
---tcatggatatgaaatgtattagatatttttaggcttcgcatcatgcagtatgtgagggcgattatggtcttattggagatgccgtcttgtgatcatgcagGAACCACCGTGGTCTTCGTCACTACTGGGGCTTGCGTGTACGTGGTCAACACACCAAGACAACTGGAAGACGTGGTAGAACCGTCGGAGTGTCCAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S215_81V6.1 (Physcomitrella patens), 3'ss of exon 3

tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgt-ttatgtagttcctaagtta----acagtcac--atattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
      |    |||   | |   || ||| | |  | ||  |  || | || ||||| | || | |||    |  ||  |  | ||      |  |||   ||||||||||||||||||||| ||||||||||||||| | ||||| ||||| |||||||||||||| |||||  | || |||   || |||||||| || ||||||
------tttttttcttgtat-ggatctttttttcgtacacattcttttcttttgtagattcttaattactctaatgttgctgaaatcaatggccgcttatgttgcagGAACCACCGTGGTCTTCGTCACTACTGGGGCTTGCGTGTACGTGGACAGCACACCAAGACAACTGGACGTCGTGGACGGACCGTTGGTGTGTCTAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 3

tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgtttatgtagttcctaagttaacagtcacatattcgcatcttcttggtttg-cagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
                             | | || |  | ||  | |  ||     || |  |   |  |  |   |||  | ||||  | ||||| |||||||||||||||||| |||||||||||||| || || ||||| || ||||||||||||||||| ||  | || |||| ||| || || ||||||||||||
-----------------------------gcaagccgtttttccctttcaat----ctcttggg--gatgg--atggattgacttctttattgtttgacagGAACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGGACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4

--tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgtttatgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG
   ||    | |||  | |   | ||       | ||      |  ||   | |  |  || || |   |  |    ||   |      |  |  |    ||| ||||||||||||| |||||||||||||| || || ||||| || ||||||||||||||||| |   | || |||| ||| || || ||||||||||| 
ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatctcttacg--gatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|211089362|gb|FL471083.1|FL471083

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|37381523|gb|CF627656.1|CF627656

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|166698578|gb|EG294764.1|EG294764

EST:     TCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: TCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|113703829|gb|EE681333.1|EE681333

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|37390184|gb|CF632319.1|CF632319

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|31910521|gb|CD651465.1|CD651465

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|166549602|gb|EG143007.1|EG143007

EST:     GGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: GGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|19351624|gb|BM896156.1|BM896156

EST:     GCCCTCGACATGAAGCTCA-GGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCG-GGTCTGCGTCACTACTGGGACCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|40336066|gb|CK370136.1|CK370136

EST:     GAAGCTCAGGGACCACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: GAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|87153623|gb|DY398412.1|DY398412

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGACCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|60336770|gb|DN203743.1|DN203743

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|22491168|gb|BU051091.1|BU051091

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCCCCGTGGTCTGCGTCACTACTGGGACCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|211002123|gb|FL462029.1|FL462029

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTTCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|78105880|gb|DV524298.1|DV524298

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|31910523|gb|CD651466.1|CD651466

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACNCG-GGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGC
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCAC-CGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGC

EST: gi|45568227|gb|CK985964.1|CK985964

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|5608255|gb|AI901922.1|AI901922

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCCCCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

EST: gi|37374390|gb|CF623548.1|CF623548

EST:     GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA
genomic: GCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCA

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 774

ACAGGAAGAAGGATTACAAGGACGGAAGGTTCTCACAGGTCGTCTCCAACGCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatt ... tggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 473

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 432

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgtttatgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG

                 agttaac  putative branch site (score: 274)
                                     catcttctt  putative PPT
               taagttaa  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgtttatgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - gccttca
- - - - - - - - - - - - - - - -atgctgc