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

...tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG

Basic information

species	Zea mays
transcript	GRMZM2G110983_T03
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 5

tgccat-cgctgtttatgaattattatgatgttcttaaaccatctgtg--ctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
  | || |    || ||| | |   | ||  ||   | |  |   |     | || | |  |     |  ||    |||      | |||||   |||| |||||  || | |||||||||||||| ||||| || || ||||||||||| |||||| | ||||| ||||||||||| || |||||||| |||||||| ||| 
-acaatgcatatttcatggact--caagacattgacatattacaggcaatttcattgatttaactgttcagtacttctatttcctgctttgtattatttccagTCGCTGCTTTGCGATCCAAACCCAAATTCACCTGCCAACTCTGAAGCTGCCCGCCTATTCAGTGAGAACAAGCGGGAATACAACCGAAAAGTTCGTGAGA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 3'ss of exon 5

tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG----------------------------------------------
                                             |     ||  |  | ||     ||    |||      | |||||   |||| |||||  || | |||||||||||||| ||||| || || ||||||||||| |||||| | ||||| ||||||||||| || |||||||| |||||||| |||                                               
---------------------------------------------tttcattgatttaactgttca-gtacttctatttcctgctttgtattatttccagtcgctgctttgcgatccaaacccaaattcacctgccaactctgaagCTGCCCGCCTATTCAGTGAGAACAAGCGGGAATACAACCGAAAAGTTCGTGAGATAGTGGAGCAGAGCTGGACCGCGGACTGATCCACTCCATCTAACCA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 5

tgccatcgctgtttatgaattattatgatgttcttaaacc-----atctgtgctgatggctacagtgcgtgtgtgtgactaacct----gaggtttgtgccattt----gcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
            ||||  |||||  | ||| |  ||  |      |||  || |      ||    || ||| | | | ||   |     || |   |   | |     |||||||||| | || ||||| ||||| ||||| || || ||||| ||||| || || ||||| || ||||||||||| |||||||| || | |||| | ||  
------------ttatatattatcttcatgattctactctttggtatccctgttatatagtagtcagcatgt-tataattattttctgaaagatacatattactctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGGGAGTACAATCGAAGAGTTAGAGAAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G16160.1 (Glycine max), 3'ss of exon 6

------tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
      | |  |  || ||  | ||     || ||  | || |    |   |     ||| | |  |||   | | | | |||  ||   ||  ||    |||||||||||| |||| ||||||||||| ||||| || || || |||||||| || || |||||||| || |||||||| || |||||| | | ||| || ||| 
agtgtgttcttttactcttcctcaacaggaat-atagtgttgacttgtacattgctctggattct-tgctattttttcattaaattggctttcttg----ttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGTGAAAACAAGCGTGAATACAACAGAAGAGTACGTGAGA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G20310.1 (Glycine max), 3'ss of exon 4

tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtga-ctaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
    ||  |     || ||| |     ||       | ||  || ||| |  | |  || |   |   | |   ||||   |   |||    | ||||||||||||| | || ||||| ||||| ||||| || || ||||||||||| || || ||||| || ||||||||||| |||||||| || | |||  ||||  
-tttatttcctgaaataaataaaatatatagcaagtatcctgctatgcagtagtcatcattttataattattttctaaaaggtaattttcctcctttgcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCTGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGTGAGTACAATCGAAGAGTGAGGGAAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 5

tgccatcgctgt-ttatgaattattatgatgttcttaaaccatctgtgc--tgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
     | | | |  | |   | | ||  ||  | |||    || ||| |  || |    |   |   | | | | |||||  || | |   | |   ||||||||||||||||| ||||||||||| ||||| || || || |||||||| || || ||||||||||| |||||||| || |||||| | ||||| || ||| 
--gtgttgttttactcttcctcaatagaatagtgttagttgatttgtacattgctctggattcttgttatttatcactaaattg-gctgctttcttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGCGAAAACAAGCGCGAATACAACAGAAAAGTACGCGAGA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G16160.3 (Glycine max), 3'ss of exon 6

-----tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG-
     | |  |  || ||  | ||     || ||  | || |    |   |     ||| | |  |||   | | | | |||  ||   ||  ||    |||||||||||| |||| ||||||||||| ||||| || || || |||||||| || || |||||||| || |||||||| || |||||| | | ||| || |||  
gtgtgttcttttactcttcctcaacaggaat-atagtgttgacttgtacattgctctggattct-tgctattttttcattaaattggctttcttg----ttgcagtCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGTGAAAACAAGCGTGAATACAACAGAAGAGTACGTGAGAT

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G01270.1 (Glycine max), 3'ss of exon 5

tgccatcgctgtttatg--aattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttg-cagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
   ||| |     |||   | || || |  |  | || |    | | |  |  |    |   |     | | |  || |   |   ||  | |  | || ||||||||| | || ||||| ||||| ||||| || || ||||| ||||| || || ||||| || ||||||||||| |||||||| || | |||  | ||  
-atcattggcacatatatcagttgttttacttgtattca-tggtgtatagtagtcagcatgttataattatttt-ctgaaaggtaattattactctgtggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGTGAGTACAATCGAAGAGTGAGAGAAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G34170.2 (Glycine max), 3'ss of exon 5

tgccatcgctgtttatgaattat-tatgatgttcttaaaccatc-tgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
 |  ||        || ||  |  |||   |   |||  |     |||  | ||    |   |     | | |  ||||   |   |||    | ||||||||||||| | || ||||| ||||| ||||| || || ||||||||||| || || ||||| |||||||||||||| || ||||| || | |||  ||||  
-gaaataaaaaaaaataaaaaaagtatatagcatttatcctgctatgtagtaatcatcatgctctaattatttt-ctaaaaggtaattttcctcctttgcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCTGAAGCAGCTCGAATGTTTAGCGAGAACAAGCGTGAATACAATCGAAGAGTGAGGGAAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 6

tgccatcgctgtttatgaattattatg-atgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatt--tgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
    ||   ||   |  |   |  ||  ||||| |    ||| | || ||  ||     | |   |   ||||     |   |   ||||    ||  | |||||| || | || ||||| ||||| || ||||||||||| || ||||| || || ||||| || ||||||||||| ||||||||| | | ||| || ||  
---gatgtttgaacagaatcaaacatatatgttttggttccagcagtccttttgatattactagcttgatgtggtcttctgaatccttgttttgttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCACGGATGTTTAGTGAGAACAAGCGCGAGTACAACAGAAGAGTCCGTGAAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0032g00310.t01 (Vitis vinifera), 3'ss of exon 4

tgccatcgctgtttatgaattattatgatgttc-ttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggttt---gtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
 | ||||  |  | |  |     | | || |   ||| |  || | ||    | ||    | | |  | |   | |   |  || | |    ||   | | |||||  || | || ||||||||||| || || || || |||||||||||||| ||||||||||| ||||| ||||| || |||||| | | ||| || ||  
-gacatc--tagtgagcagcagctttaatttcagttacaatattt-tgtcagttgcctgtgagggcatattctaatgggcatagttcttaaatgttttatccagTCCCTGCTCTGTGATCCAAACCCAAACTCACCTGCAAACTCTGAAGCCGCACGCATGTTCAGTGAGAATAAGCGGGAATACAACAGAAGAGTGCGTGAAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 3'ss of exon 4

-tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgt-gtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
          || |       |  | ||   ||      |    |  |  || | | ||  ||||| | | | || ||  || |     |       ||||||| ||| ||||||| |||||||||||||| || || ||||| || || |||||||||| |||||||||   ||| ||||||||||| |  || || ||| 
agcttgagattggtcggcgtcttctttggcatttgcgg-ctgaatacgtcgacgacaacgatgcgtagagcgagatta-tctaatacacggctttgatgcagTCTTTGCTGTGCGACCCAAACCCGAATTCACCAGCGAACTCGGAGGCTGCCCGCATGTACAGCGAGAATCGGCGTGAGTACAACCGGAGGGTACGCGAGA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 3'ss of exon 4

tgccatcgctgtttatgaattattatgatgttcttaaaccatct--gtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
 || |  |  | |      || ||     ||    |  | | |   | | ||||| | ||  ||||||   |    |   || |    ||       ||||||| ||| | ||||| |||||||||||||| || || ||||| || || || ||||||| ||||||||||  ||| || || ||||| |  || || ||| 
-gcgagagtggatggcttcttctt-cagcgtgtgcagccgaacacagcgatgatgacgacgatgcgtgaaagctgtttctctaacacgtggctttggtgcagTCTTTGCTATGCGACCCAAACCCGAATTCACCAGCAAACTCGGAGGCTGCTCGCATGTACAGCGAGAACCGGCGTGAATATAACCGGAGGGTACGCGAGA

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|31998321|gb|CD662030.1|CD662030

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|211368006|gb|FL470437.1|FL470437

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|37400480|gb|CF637593.1|CF637593

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|50323647|gb|CO518773.1|CO518773

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|18166186|gb|BM336025.1|BM336025

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|40334943|gb|CK369013.1|CK369013

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|14244483|gb|BG842475.2|BG842475

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|37376281|gb|CF624651.1|CF624651

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|37384502|gb|CF629329.1|CF629329

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|37390719|gb|CF632593.1|CF632593

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|33104117|gb|CF064077.1|CF064077

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCACTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|149108750|gb|EE189816.2|EE189816

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|16920335|gb|BM074609.1|BM074609

EST:     CCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: CCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|37393932|gb|CF634233.1|CF634233

EST:     CACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: CACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|148995969|gb|EE035217.2|EE035217

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|18166104|gb|BM335943.1|BM335943

EST:     CCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: CCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|211248410|gb|FL329620.1|FL329620

EST:     TCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: TCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|32846308|gb|CD985989.1|CD985989

EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

EST: gi|7216375|gb|AW562497.1|AW562497

EST:     AGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: AGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC

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: 211

TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 287

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG

                          gactaac  putative branch site (score: 287)

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG