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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACATGGCCTTGGCTGTGAAAAATCCATGCCATCTCAATATGGCTGCATGCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttactcgaccatgcccataagtacattcagtcttgaacccacgatttacattcatgggtacatttttacagtttacggctttgcatagaccttag...

Basic information

species Zea mays
transcript GRMZM2G133624_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133624_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g05090.1 (Oryza sativa), 5'ss of exon 6
AGACATGGCCTTGGCTGTGAAAAATCCATGCCATCTCAATATGGCTGCATGCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttactcgaccatgcc-cataagtacattcagtcttgaacccacgatttacattcatgggtacatttttacagtttac-ggctttgcatagaccttag-
|||||||||||| |||||||||||||| ||||||||||| ||||| ||||||||||||||||| |||||||| ||||||||||| || |||||||  ||||||||||| ||  | |     |||||    ||| | ||||  || || | ||||   | |   ||| |     | |    || |  ||||  | | | ||   
AGACATGGCCTTAGCTGTGAAAAATCCCTGCCATCTCAACATGGCCGCATGCCTGATCAAACTGAAGAGATTTGATGAAGCTATCGCACAGTGTACAATTgtatgttattcttctacattgcataaa---atttactcttacactcatgctttaacattacatgtataacacaagaaaaaactgaatttgatttgtcattcag

upper sequence: GRMZM2G133624_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv13s0064g00580.t01 (Vitis vinifera), 5'ss of exon 7
AGACATGGCCTTGGCTGTGAAAAATCCATGCCATCTCAATATGGCTGCATGCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttactcgaccatgcccataagtacattcagtcttgaacccacgatttacattcatgggtacatttttacagtttacggctttgcataga-----ccttag
 |||||||| ||||||||||| ||||||||||| || || ||||| ||||||||||| || || ||| | | ||| ||||| ||||  || || ||||||||||||   |   |  ||   | || | |||    |||       | | |||  |||  |     ||| | |  |   ||| |  | | | |       ||||  
TGACATGGCTTTGGCTGTGAAGAATCCATGCCACCTTAACATGGCAGCATGCCTGATAAAGCTGAAGCGCTACGAAGAAGCCATTGGTCAATGCAGCATTgtatgta--taatctttgtggacaaat-catgtcttctattttatatgcttttgattgttcttatcatctctggaaactacagtgtggaagaagaaaatcctt--
















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|78025886|gb|DV494273.1|DV494273
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|29130064|gb|CB380768.1|CB380768
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|60357904|gb|DN224877.1|DN224877
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|78108737|gb|DV527154.1|DV527154
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|18661183|gb|BM501275.1|BM501275
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|71299220|gb|DR785608.1|DR785608
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|37377161|gb|CF625161.1|CF625161
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|6827692|gb|AW331335.1|AW331335
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|71768316|gb|DR966253.1|DR966253
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|44901180|gb|CK827725.1|CK827725
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTNGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|71756680|gb|DR954617.1|DR954617
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|12973805|gb|BG268675.1|BG268675
EST:     ACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: ACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|71306392|gb|DR789337.1|DR789337
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|71435312|gb|DR816362.1|DR816362
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|71768315|gb|DR966252.1|DR966252
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGGGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|76021435|gb|DT948605.1|DT948605
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|6403345|gb|AW171820.1|AW171820
EST:     AGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: AGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|6526795|gb|AW216068.1|AW216068
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|6466744|gb|AW191404.1|AW191404
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|71299221|gb|DR785609.1|DR785609
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAAT
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAAT
EST: gi|60401366|gb|DN234173.1|DN234173
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|71759248|gb|DR957185.1|DR957185
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|211149718|gb|FL467074.1|FL467074
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATT                         GTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
EST: gi|32864225|gb|CF003907.1|CF003907
EST:     GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCA-T                         -TTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA
genomic: GCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttact ... tattattcagGTTTTGACAGAAGATGAAAGTAATGTCAAAGCGCTGTTCAGGCGAGGAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACATGGCCTTGGCTGTGAAAAATCCATGCCATCTCAATATGGCTGCATGCCTGATCAAACTAAAGAGATTCGATGAAGCTATTGCGCAGTGTAGCATTgtatgttactcgaccatgcccataagtacattcagtcttgaacccacgatttacattcatgggtacatttttacagtttacggctttgcatagaccttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC