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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatggcatattgctatctcttcttcattcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC

Basic information

species Zea mays
transcript GRMZM2G176604_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g03410.1 (Oryza sativa), 3'ss of exon 2
gtatgatggcatattgctatctcttcttca-ttcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
        | | | ||  |||||||| ||| ||  || |  |   |    ||||| | ||           |||||| |  | | ||    || || ||| | || |||||||||||||| ||||| || ||||| ||||| || |||||||| || ||||||||||||||||| || ||||| ||||||||||| ||||| ||||||||||||
--------gtacaatgaaatctcttcatcaattttgtgcattattattccctctctgatt-----------aatggatgttttactca---cattgccgttt-tggttgaacagGATGCTCGTGTATGAATATGTAGACAACGGCAATCTTGATCAATGGCTTCATGGTGATGTAGGGGAAGTGAGCCCACTAACTTGGGAAGTCAGGATGAAC

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 2
gtat-gatggcatattgctatctcttcttcattcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
|||| |||  | | ||    |     ||  ||           |    | || ||| ||| |  | |   |          |||   |||  | ||| ||   || ||  |||||||||||||||| |||||||| |||||||| ||||| || || ||||| ||||| || |||||||  ||||||||  | |||||| || |  ||||||||
gtattgatatcttcttctcttaaaaactaaatagaaaaaaaaaattgatgctatcaattttg--tttggtttgacatgatgtgagatctga-agtgtggtac-tgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G03650.1 (Glycine max), 3'ss of exon 2
gtatgatggcatattgctatctcttcttcattcggtccggtgacacc-tactctcagtttggattctcaataatggaag-cctgattcctgtcac-tgtcgtctatgcttgaa---cagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
       |   | ||  | | | || ||||||  |  |  |||  |  ||   |  |||| |  | | || |||| |||   |||    ||     |||  || ||| |   |   ||||||||||||||| || |||||  ||||||| ||||| || |||||||||||||| |||| ||||   ||||||||| | ||||||||  || | ||||||
-------gtattttttttttttttttttcattttgaacattgaagctataaagtttgtttag--tttaaagaatgtaagatttgaactttgaagtatgtattcaatgttcatattgcagGATGCTTGTGTATGAATATGTCAACAATGGGAATCTAGAACAGTGGCTTCATGGGGATGCTGGACCTGTAAGCCCAATGACATGGGATATCCGAATGAAC

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G47170.1 (Glycine max), 3'ss of exon 2
gtatgatggcatattgctatctcttcttca---ttcggtccggtgacacc--tactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
           ||||| | |||  |||| |    |          | |    | || ||| ||| | |       |   || |   ||||      | ||| | |  || ||  |||||||||||||||| |||||||| |||||||| ||||| || || ||||| ||||| ||||||||||  ||||||||  | |||||| || |  ||||||||
----------gtattgatttcttctcttaaaaactaaaaagaaaaaaattgatgctatcaattttgttcggtttgacaagatgtaagatttga---agtgt-ggcactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAACAATGGCTGCATGGGGATGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G07250.1 (Glycine max), 3'ss of exon 3
gtatgatggcatattgctatctcttcttcat-tcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
        | |||||  | | | || |  |  | |   |    | |  |  | |   ||         || | | |||   |||    |||        |  ||  |    ||||||||||||||| || ||||| |||||||| ||||| || |||||||| ||||| |||||||||   ||||||||| | ||||||||  || | ||||||
--------gtatatttttttttgttttgaacattgaagctaaaagagtttgtttggtttaaagaatgtaagatttgaactttgaaggatgtattcaatattcatatt---gcagGATGCTTGTGTATGAATATGTTGACAATGGGAATCTAGAACAGTGGCTGCATGGGGATGTTGGACCTGTAAGCCCAATGACATGGGATATCCGAATGAAC

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT1G01540.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgatggcatattgctatctcttcttcattcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
                             ||     ||| || | | ||       |  ||  |  ||| |  |    | |||  |||    |||   ||  | ||   | |||||||| ||||| || | ||| |||||||||||| | || || ||| |||| ||||||||||| || || ||||| ||||| |||||  |  | ||||| 
---------------------------gtatatataccgctg-ctcgtatctcttttccggtgttacaaaagcgatgtcgtga--cctaatgctgggttcgttact---atagGATGCTCGTGTATGACTTTGTCGACAATGGTAATTTGGAGCAATGGATTCACGGTGATGTTGGCGATGTCAGCCCGCTAACTTGGGATATACGTATGAAT

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 3'ss of exon 2
gtatgatggcatattgctatctcttcttcattcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
           |||||||| |  |  |    |   |||  ||||||    | |   |  |||| |  || | |   |   |     || ||| | |  | | |  |||   |||||||||||||| ||||||||||||||||||||| | ||||||||||||||||| ||||| || ||||| ||||| || ||||||||  |  |||| |||
----------gtattgctacccatcttctgctaaatcc--tgacactgggttttcttgaggatccaaaaaactaacattttttcatctttcatt-tgttttttttttgtctagGATGCTTGTGTATGAGTATGTGGACAATGGTAATTTGGACCAGTGGCTTCATGGGGATGTAGGGGAAGTCAGCCCTCTGACATGGGATATTCGGATTAAC

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatgatggcatattgctatctcttcttcattcggtccggtgacacctactctcagtttggattctcaata-atggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
              ||  | |  || ||| | |   | || |        |  |||      |     | |  || ||  || | | | ||| ||   |     ||||    |||||||||||||||||||| ||||||||||| ||||| || |||||||| |||||   | |   | ||  || | ||||  ||||||| |   | |||   
-------------gtga-agcatttattcttcccacctggagtttttgtgtgccagcacaattctcttacacgtgcaatgctaacttc-gtctctcgtg-----gcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 2
gtatgatggcatattgctatctcttcttcattcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
             |   | ||    |||| | | | || ||         |    |    | | ||  ||  |    |  |||   | ||  |||  | || |       ||||||||||||||||||||| ||||| ||||| ||  | || |||||||| |||||   | |     ||  ||   ||||  ||||||| | | | |||   
------------gtgaatgtcatcccttcttcctgcccagtt-tgttgtgtggtggcgcagctccttgatgttctttgt-tgacctc-gtttctggtggctgtt-----gcagGATGCTTGTGTACGAGTACGTGGATAATGGAAACTTGGAGCAGTGGCTGCATGGACCTCTGTCCCAAACAAATACACTTCCATGGGAAGCCCGCATGCGG

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ27863 (Selaginella moellendorffii), 3'ss of exon 3
gtatgatggcatattgctatctcttcttcattcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
                                                      |  | | ||||||    ||| |||     ||  |  |  ||         |||  |||||||||| || || ||||| || |||||||||||||| || ||||||||||| ||    |         | | | | | ||||||||| || |||||||| 
----------------------------------------------------gtacgtcgaattctc----atgaaag---agtttttcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAGGTTAGGATGAAA

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
gtatgatggcatattgctatctcttcttcattcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatg--cttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
                                                      |  | | ||||||     || |||    |||  | ||||| | |   | |  |||  |||||||||| || || ||||| || |||||||||||||| || ||||||||||| ||    |         | | | | | ||||||||| ||  ||||||| 
----------------------------------------------------gtacgtcgaattctc----gtgaaag----attttt-tcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA

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|60352421|gb|DN219394.1|DN219394
EST:     CACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCTTACAG                         GATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCA
genomic: CACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCTTACAGgtatgatggc ... gcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCA
EST: gi|60394580|gb|DN227450.1|DN227450
EST:     CACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCTTACAG                         GATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCA
genomic: CACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCTTACAGgtatgatggc ... gcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 126

AGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCTTACAGgtatgatggc ... gcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

AGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCTTACAGgtatgatggc ... gcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

AGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCTTACAGgtatgatggc ... gcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 400

AGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCTTACAGgtatgatggc ... gcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
                   gcctgat  putative branch site (score: 400)
       tcaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatggcatattgctatctcttcttcattcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG