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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgctgttacag

Basic information

species Glycine max
transcript GLYMA03G40290.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgct----gttacag
|     |||||||||||||||||||||| ||||||| ||| || || ||||| ||||| ||||||||||||||||| || ||||| || || |||||||||||| | || |     |||   ||  |           | ||| | | |||  | |   || | |     || ||   |  | |  | |||  |     ||||||
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtctgataatcagttttactggcaacccttgtgg-tttcttttagatgaaaatatttatgtatatggcttcctgatattcttcattcattttacag

upper sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactactt-gctgttacag-----
|     || |||| ||||||||||| |||||||||||||| ||||| ||||| ||||| ||||||||||| || || ||||| || ||| | || || ||||| ||    || |    |   | ||   |   || | ||  |||    ||  | | |||  |      ||    |  || |    |  || |   || ||      
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaat----tataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag

upper sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 5'ss of exon 8
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgta--tatcctctaaacaaatttcttcaagctaa--gctatatatggatctatttggggtagtaac----actgtctaatttgatatattaaactacttgctgttacag---------------------
|     || ||||||| ||||| || || ||||||||||| ||||| ||||| || ||||| ||||||||||| || ||||| || ||  | || ||||||||  |||| |         ||||  ||| || |    |  || |  || | |||    |  | |     | | | || ||    | |||      |   ||| | |                       
TGCTTGATTTGAGTGGTATTCTTACGGTGTTCTTCTGTGGTATTGTAATGTCGCACTATACCTGGCATAATGTAACAGAGAGTTCCAGGGTCACAACCAAgtaagtatctttatggtttgtttcagcaaacttattattccattttcatttttttaacttgatgatttcaaatatgtatttcctgaaattgtgtatcacactgatgcttctctaattgtatactctatag

upper sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 7
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgctgttacag--
|     |||||||||||||||| || ||||||||||| || || || ||||| ||||| || ||||| |||||||| |||||||| ||| | || ||||||||  |  ||      | ||| |      |||  | | | |   |||  ||     |  ||  ||| || | ||    | ||   |   || |  | ||    
TGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATGTCGCATTACACCTGGCACAATGTGACAGAGAGCTCAAGAGTCACAACCAAgtaattattccttgtcattttttcgctagtaatgtttctgt---tctgcttaataaacgaatgctgactgaatt--ccttttgggcctttttcattcacttag

upper sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcct--ctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgc-tgttacag
| | | | |||||||| ||||| ||||| ||||||||||| || || ||||| ||||| ||||||||||||||||| || || || ||  | || ||||||||| || |  ||  |   | || ||| ||| ||  |   ||||| |||   |       | |      ||||||    || ||   ||  || | |||| |||
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttctggattcagtttttctagcaaaaat---tatggttcttacttcttacattatgtatactaattgctgatttt---ctctttccatgttgcag

upper sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G311165_T01 (Zea mays), 5'ss of exon 9
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgctgttacag
|     || ||||||||||||||||||| || |||||||| || || ||||| || ||||||||||| ||||| || || || |||||  | || ||||||||  |    | |   |  ||||  | |   |  |   | ||    |   |    | ||||  ||   ||   | || || ||   |   ||   | ||||
TGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagtagcttcat--accttctgtatggacatttgcttttgatcatgcattctttggtaatgct---tatgctaatgtacta--ttggatgg-atcacag

upper sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G311165_T06 (Zea mays), 5'ss of exon 7
------------------------------------TATGG--TATCTGAGTGGCATTCTCACTGTATTC--TTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGC----TCGAGAATAACTACCAA-
                                     ||||  ||| |   |  ||| ||  ||| | |     |  ||   || | |  |||    | | || ||||  | | |  |  | |      |  |||   ||  ||   ||   |  | ||    || ||  || |  | ||    ||    | || | |      ||   |  ||  ||| | | |   ||     |    ||| ||||
GCATTCAACCGATCATGAAGTTTCCATTATGATGCTAATGGCTTATTTATCTTACATGCTAGCTGAAgtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgtaagttgctcgatttgagtggcattctca-ctgtgtttttctgtggtatcgt--aatgtcacactatacttggcaaaatgtaacag

upper sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 5'ss of exon 9
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctct----aaacaaatt------tcttcaagctaagctatatatggatctatttggggtagtaa-----cactgtctaatttgatatattaaactacttgctgttacag--------
|||  ||| |||||||||||||||| ||||| |||||||||||||| ||||| ||||| || ||||| ||||| || ||||| || ||| | |||||||||||| |  | |    |||  ||||      | ||   |  | | | |||||   | |||||     | ||       |||| ||  | ||     || || | ||  || | | |         
TATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCAAgtatgtattttcctgaaagcaattggaacattttttggtcaggatttatat--ttttatttcaaaaaataggtcattactggctg-tatgcctgttttaatttctgtctataaaatttccacag

upper sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S113_117V6.1 (Physcomitrella patens), 5'ss of exon 8
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctata-tatggatctatttggggtagtaa-cactgtctaatttgatatattaaactacttgctgttacag--------------------------------------------------------
| |  ||  ||||||| || ||| | || ||||| ||||| ||||| ||||||||||| |||||||||||||| || || |  ||  |||  || |||| |||  | |  | |      ||      | |   ||||| ||  || | | | |    |  ||  | | |  |   ||||   | ||  |  | |  |||  ||                                                        
TTTTCTACTTGAGTGGAATACTCTCAGTGTTCTTTTGTGGCATTGTAATGTCTCATTACACTTGGCATAATGTCACGGAAAATTCTCGAACCACAACCAGgtacgttccttcatgcctcttagcttcgatgttctatactagcgaacgaatggcaacatcaaatattcttgagactgatgcgt-aatttcttggaggttggagttatgatactgatgcttgtcatcaacgtgacattaatgcactttggtgattcacag

upper sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S207_23V6.1 (Physcomitrella patens), 5'ss of exon 10
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttg-----atatattaa-actacttgctgttacag
| |  ||  ||||||| ||||| ||||| ||||| ||||| ||||| ||||| || ||||| ||||||||||| ||||| |||||  ||||||| |||| ||| |      || ||  | |  | || |  |      | |   || |  |||   |   |   ||| ||| ||      ||||||||| |    |||   | ||| 
TTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCAGgtaaac-----aaccatctcttctgaatcggaatgtcctgtcattcaa--tggaacacctaagttgtttaaattatagtcatatattaatatcctttgtcttaacac

upper sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S31_203V6.1 (Physcomitrella patens), 5'ss of exon 10
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctata-tatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgctgttacag--------
| |  || |||||||| ||||| || || ||||| ||||| ||||| ||||| || || || |||||||| || ||||| |||||  || |||||||||||||   | |||        |||||  || |  | | |  | |  |||||   |   |  || |  |||  |||  |  |  |  ||  |  |   | |  ||        
TTTTCTACCTGAGTGGAATTCTTACCGTCTTCTTTTGTGGCATTGTAATGTCACACTACACCTGGCATAACGTCACTGAAAGCTCACGAGTAACTACCAAgtagg-catct-------cttctttcagttgggatgtccttttcatctaacagaatttttatc--tgttgaataggccacgtacaagcagctcaagatttagtctatttg

upper sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
lower sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgctgttacag
| |  || |||||||| || ||||| || ||||| ||||| ||||||||||| |||||||| ||||| || || || |||||||| ||||| || |||||||| |    | || |    |  |      |||  |||   || |                                                         
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgacaaatctgtatcttatgttttaacttattcctgcag--------------------------------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgctgttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT