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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcctaataggataaattaagaagccatgcaaaatatatgcaatccagatgtattgttacattgcttcaatagtttcaaaggttattagtttctaattcatttggaagctcaatctttaggtgttgctttgccattttagGTTGGATCCAATGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTTGGTG

Basic information

species Glycine max
transcript GLYMA11G03580.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g01650.2 (Oryza sativa), 3'ss of exon 5
gtaatcctaataggataaattaagaagccatgcaaaatatatgcaatccagatgtattgttacattgcttcaatagtttcaaaggttattagtttctaattcatttggaagctcaatct--ttaggtgttgctttgccattttagGTTGGATCCAATGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTTGGTG
                                         ||   |||   |  ||  ||    | | |   |||||   |   ||  | || | |   ||||| ||  | | || ||   |  |  ||  | |   ||     ||    || ||  ||||||| ||||||||| | |||||| ||||| | |||||||||||||| || |||| |||||| ||||||||||  |||||||   
---------------------------------------cttgacttcccattccatgattttcatacattt-tagttctcatcttttatcgtgtgtggatcattagg--gttgaacctaacttagcatttttgttggatagGCTGTGAATTCTAAGAGCATGCTGGATGATTGGCAAGAGAATTTGGCTATTATAACTGCAAACAGGACGAAAGGTGATGATCTTGTAATTACGCACCTTG---

upper sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 5
gtaatcctaataggataaattaagaagccatgcaaaatatatgcaatccagatgtattgttacattgcttcaatagtttcaaaggttattagtttctaattcatttggaagctcaatctttaggt-gttgctttgccattttagGTTGGATCCAATGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTTGGTG
                                       | |||      |||      ||  | || |  |  |  |      ||| || | ||    || |  | |  ||||| | | ||  |  ||| |||| ||    ||  | |  | ||||||||| | ||||| |||||||||||| ||||| | ||||||||||| || || |||| ||| || || || ||||  || ||||| |
--------------------------------------ttttgcttcattgataatgcattctactgttctaccacctc-----gttgttggctttctgtttaaatagtggctcactttataattcattgttttgtcacac-agCCTAGTCCTAATGGCATGTTGGATGACTGGGAGGAGAATTTGGCTATCATAACTGCAAATAGGACAAAAGGTGACGACCTAGTTATTACCCATCTTGGAG

upper sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G442742_T01 (Zea mays), 3'ss of exon 1
gtaatcctaataggataaattaagaagccatgcaaaatatatgcaatccagatgtattgttacattgcttcaatagtttcaaaggttattagtttctaattcatttggaagctcaatctttaggtgttgctttgccattttagGTTGGATCCAATGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTTGGTG---
                                 | |||| |     ||||    |   ||     ||   ||| |   |  ||| | || |     | ||| | ||          |    |  ||||  ||| |    | ||  |||    |||   ||| | |||||||||||||||||| ||||| | || |||||||||||||| |||| ||| |  || ||||| |  || |||||||   
--------------------------------aacaataaacttcctccaataattgggtc---ctgaaacaagaagcttgaag-tcatgatgacatgattgactt-------tttttgcaatttgtttttttcctgagtcagCCTGGTCGTAAT---ATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAAAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT

upper sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G429241_T01 (Zea mays), 3'ss of exon 5
gtaatcctaataggataaattaagaagccatgcaaaatatatgcaatccagatgtattgttacattgcttcaatagtttcaaaggttattagtttctaattcatttggaagctcaatctttaggtgttgctttgccattttagGTTGGATCCAATGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTTGGTG---
                                       |      ||  ||  | | | ||       |||||| |||     |||     ||| |  || | |  ||   |   |    |  ||||  ||| ||    |  |   | |||  |   ||| | |||||||||||||||||| ||||| | || ||||||||||||||  ||| ||| |  || ||||| |  || |||||||   
---------------------------------------tgcagcttcatgacttttgggtatcacttatcaataattttcctagtt-----ttttttgtttactctgacttttttttgcaatttgttttttttcctgagtcagCCTGGTCC--TAATATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAGAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT

upper sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G163277_T01 (Zea mays), 3'ss of exon 5
---------------gtaatcct-aataggataaattaagaagccatgcaa--aatatatgcaatccagatgtattgttacattgcttcaat-----agtttcaaaggttattagttt-ctaattcatttggaagctcaatctttaggtg--ttgctttgcc-attttagGTTGGATCCAATGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTTGGTG
                |  |  | ||| |  |    | | |     |   |  ||    ||||       |   ||  | || ||     ||      || |||      | || ||| |    |  | |     ||   | ||| | |   ||| ||| ||    | ||  |||  | ||||| ||| | |||||||||||||||||| | ||| | || |||||||||||||| |||| ||| || || ||||| |  || |||||||
gtacttgcaaagttaatggtttttaattgtttttgctgacattttgtttgattaacgattgcataatgtcttgtttactgcagtgtcatgatttttgggtatcacttaccaataattttcctgcttttctatttactttcttttttgataatttgtttttcctgagtcagCCTGGTCCTAATGGTATGTTGGATGATTGGGAGGAGAATTTAGCTATTATTACTGCAAACAGAACGAAAGGTGACGATCTAGTAATCACCCATCTTGGTG

upper sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 5
gtaatcctaataggataaattaagaagccatgcaaaatatatgcaatccagatgtattgttacattgcttcaatagtttcaaaggtt-attagtttctaattcatttggaagctcaatctttaggtgttgctttgccatttt-agGTTGGATCCAATGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTTGGTG
                                         | | | |   |  | |||  | |  | ||| || || ||   |  | |  |   |||   ||  |  |   |||  |||  |  | ||  | ||  ||||  || ||||  | ||| | ||||| || |||||||| |||||| ||||||| |||||||| || ||||| |||||||||||||||||| ||||||| ||||| |
-----------------------------------------ttcgaccttaacattttgcaaaa--gtttctattgtatctttgcctcaacaagctct--ctctctctgtgtctctctctcaatcttttcttatgaaatttccagTTTGGGGCTAATAGTATGCTAGACGATTGGGAAGAGAATTTGGCTGTGATAACTGCCAATAGAACAAAAGATGATGAACTTGTACTTATTCATCTTGGAG

upper sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 6
gtaatcctaataggataaattaagaagccatgcaaaatatatgcaatccagatgtattgttacattgcttcaatagtttcaaaggttattagtttctaattcatttggaagctcaatctttaggtgt--tgctttgccattttagGTTGGATCCAATGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTTGGTG
                                     | | ||  |||     ||  ||  |   | |||| | | |||     |  |||    | |  || |    |    |  |  ||| | | |  ||   |||   | | || |||  | ||  | ||||| ||||| ||||| |||||| ||||  |||||||||| |||||||| ||||||||||| ||||| |||||||| |      
-------------------------------------tgtgtggtatcagttagttgtgaaatgattcttctaaaattttctttggcatt--cctttgcttgagcaagtctattgagtttttgttttaatggcctgcagATATGGGCTGGGGCAAACAGTATGCTAGATGAATGGGAAGAGAATTTGGCCATAATAACTGCTAACAGAACAAAAGATGATGAGCTTGTTATTATTCATC------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtttctaattcatttggaagctcaatctttaggtgttgctttgccattttagGTTGGATCCAATGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTTGGTG
     ttctaat  putative branch site (score: 2)
                                         ctttgcc  putative PPT
        taattcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcctaataggataaattaagaagccatgcaaaatatatgcaatccagatgtattgttacattgcttcaatagtttcaaaggttattagtttctaattcatttggaagctcaatctttaggtgttgctttgccattttagGTTGGATCCAATGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG