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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattaataaggctattttcttcttattcatttattggaacttgctactttacaccaagatgaagaaagtgatttttcaatcgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT

Basic information

species Glycine max
transcript GLYMA09G38110.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 7
-----aattaataaggctattt-tcttcttattcatttattggaacttgctactttacaccaagatgaagaaagtgatttttcaatcgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT---
     |     ||  || ||||  ||  | |||  |||    | |     |  ||| || |  | ||||  |      || |     ||    | | ||| | |||||||| |   |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| || || || || ||||||||||| ||||| ||||| || |   
atggtatgctgtagagcaatttacctgttcatttttttccatggagacatt--tttgcatc--gctgaatca--ctgcttatttgctgattacttttaatctccagGGTGGTG---AAGATGACAACTTTGCTATCGTGTTTGCTGCTATGGGAGTGAATATGGAAACAGCCCAATTCTTCAAACGTGATTTTGAAGAGAACGGGTCAA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 7
aattaataaggctattttcttcttattcatttattggaacttgctactttacaccaagatgaagaaagtgatttttcaatcgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT---
 | |   | | | |  ||| | |    ||||   |   | |   | |||||||     |   |     | ||   |   ||  | |||   ||  | |||||||| |   |||| ||||| ||||| || |||||||| ||||||||||| |||||||| || || || || ||||||||||| ||||| |||||||| |   
tactgtaaggtcaacattcatatggagcattgtgtattaatgtatgctttacatgtctaaatatggcttaatcactgcttctgatttttgtaacctgcagGGTGGTG---AAGATGACAACTTTGCTATTGTGTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAATGGTTCCA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 7
aattaataaggctattttcttcttattcatttattggaacttgc-tactttacaccaagatgaagaaagtgatttttcaatcgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT---
      | |||  |   | |   |      || |     | ||  | |||||||         |     |  |   |   ||  | ||| | |   | |||||||| |   |||| ||||| ||||| || |||||||| ||||||||||| |||||||| || || || || ||||||||||| ||||| ||||| || |   
ttcctgtgaggtcaacatttatatggaggattgtgtattcatgtatgctttacatgtcttaataaggcttagtcactggttctgattttattacc-tgcagGGTGGTG---AAGATGACAACTTTGCTATTGTGTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 7
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 8
---aattaataaggctat-tttcttcttattcatttattggaacttgctactttacaccaagatgaagaaagtgatttttcaatcgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT---
     || ||  ||  |  | |    | | |   |  |||     ||| |   |  |  |     || | |||      |   || |  | ||| ||| | |||  |      || || || || || ||||| ||||| ||||| ||||| || ||||||||||||||||| ||||| |||||||| || ||||||||||| |   
ctcctttgatttggtaaaatctacaatgagttggtagttgtgtaatgccataatgtattat----aaaacagtatcacattggtccatttatgtgaatttgcagCATCAG---GAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 7
-aattaataaggctattttcttcttattcatttattggaacttgctactttacaccaagatgaagaaag---tgatttttcaatcgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT---
 |  | | | | | ||||  ||| | || ||||     |  ||  | ||||  | |||  |  |    |   |||  | ||| |       | | ||  | |||| ||     ||||||||||| |||||||| || ||||||||||||||||| ||||||||||||||||||||||| |||||||| || ||||| ||||| |   
gatgttaaatgaccatttatttcctttttatttt----attttctttctttttatcaattttgaacttgctatgagatatcatttttctacttttaacttgcagGATGTG---GAAGAGGACAACTTTGCCATTGTTTTTGCAGCTATGGGAGTAAACATGGAGACTGCACAGTTTTTTAAACGTGATTTCGAGGAAAATGGATCAA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 7
aattaataaggctattttcttcttattcatttattggaacttgctactttacaccaagatgaaga--aagtgatttttcaat---cgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT
        | ||  || |  | |||||  |||  | ||      | || ||  |   || |       ||| ||  |  |||       | |  ||  |  ||||| || |   |  || ||||||||    || || ||||||||||||||||||||||||||||| ||    || ||||||||||| || ||||| || || |
-----cctaagcatttgttcttttattggtttggttgataccttttctataagcgtggaaggctcctgagtaatgataaaatgtgttggcgtgttccttcgacagGATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGT

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 7
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
aattaataaggctattttcttcttattcatttattggaacttgctactttacaccaagatgaagaaagtgatttttcaatcgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT---
                         | || || ||       | |  | | |     | ||  || | ||||         ||  ||  |   ||| ||| |||  |  |||   ||||| ||||| ||||| |||||||||||||| || ||||||||||||||||||||||||||| | || |||||||| ||||| |   
------------------------gtacaattgttt---tccgtttatcttctgtctgttgttgagactgat---------gagtttctttcgtatccagCGTGATGTTGAA---GACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 7
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 6
aattaataaggctattttcttcttattcatttattggaacttgctactttacaccaagatgaagaaagtgatttttcaatcgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT---
              |  | || || | | |||||       | ||   |        | ||  || | ||||         ||  ||  |   ||| ||| |||  |  |||   ||||| ||||| ||||| |||||||||||||| || ||||||||||||||||||||||||||| | || |||||||| ||||| |   
-------------gtacttttgttttccgtttatc------ttctgtct--------gttgttgagactgat---------gagtttctttcgtatccagCGTGATGTTGAA---GACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGAGATTTTGAGGAAAATGGATCGA

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|18734533|gb|BM528238.1|BM528238
EST:     GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAG                         GGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTT
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAGgtatatacaa ... caatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTT
EST: gi|22931741|gb|BU548880.1|BU548880
EST:     GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAG                         GGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTT
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAGgtatatacaa ... caatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTT
EST: gi|14259630|gb|BG882538.1|BG882538
EST:     GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAG                         GGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTT
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAGgtatatacaa ... caatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTT
EST: gi|8285807|gb|BE023366.1|BE023366
EST:     GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAG                         GGTGGAGGAGAAGAGGACAATTTTGCCATTGTGTTTGCAGCTATGGGAGTT
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAGgtatatacaa ... caatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTT
EST: gi|5342420|gb|AI794704.1|AI794704
EST:     TCAGGCTGGCTTAGTCAAGCGACTACGAAA-GTCTGATCATCTTCTCGAG                         GGTGGACGAGAAGAGGAC
genomic: TCAGGCTGGCTTAGTCAAGCGACTA-GAAAAGTCTGATAATCTTCTCGAGgtatatacaa ... caatatacagGGTGGAGGAGAAGAGGAC
EST: gi|16279376|gb|BI943404.1|BI943404
EST:     GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAG                         GGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTT
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAGgtatatacaa ... caatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTT
EST: gi|7589581|gb|AW705352.1|AW705352
EST:     GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAG                         GGTGGAGGAGAAGAGGACAATTTTGCCATCGTGATTGCAGCTATGGGAGAT
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAGgtatatacaa ... caatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTT
EST: gi|16283538|gb|BI945603.1|BI945603
EST:     GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAG                         GGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTT
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAAAAGTCTGATAATCTTCTCGAGgtatatacaa ... caatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttacaccaagatgaagaaagtgatttttcaatcgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT
                                       ctttgtc  CT-rich tract
                         atttttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattaataaggctattttcttcttattcatttattggaacttgctactttacaccaagatgaagaaagtgatttttcaatcgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA