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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attatgtcagatcaataaaagaaagcagtgatttatttcattctaaagggtcagtaaaataggctaatcttttttttttttttcttttaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG

Basic information

species Glycine max
transcript GLYMA08G37270.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0211g00090.t01 (Vitis vinifera), 3'ss of exon 4
-attatgtcagatcaataaaagaaagcagtgatttattt-cattctaaagggtcagtaaaataggctaatcttttttttttttttcttttaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG
 | ||| | |||    |       |    | |||||| |  ||| |  ||  |   | | | |    ||       | ||| ||    ||     ||| |||||||||||||||||||||||||| |||||||||||| | |||||||||| |||||| |||||||| ||||||||||||||||| |||||||||||| |||
aaatatatgagagttgttggctccatt--taatttatgtgtattatttagcttttattataaaaaggaagagccactatttcttatgattttctctgttcagGGTATTGATGGCTCCAGAGTTGAAAAGGTGTTGGAATCTGTTCATATTGTAGCTAACAAAAACACCGTTCCTGGAGATGTGTCGGCCATGGTTCCTAGTG

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 12
-attatgtcagatcaataaaagaaagc--agtgatttatttcattctaaagggtcagtaaaataggctaatcttttttttttttttcttttaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG
 | ||  | |||    |       |    | | || | | |||||            |||||  |   |  |  | ||| || |   |||      ||| |||||||||||||||||||||||||| |||||||||||| | ||||||||||||||||| || ||||| ||||||||||||||||| ||||||||||||||||
aaatagataagagttgttggctccatttaatttatgtgtatcatttagcttttattataaaaaggaagagccactatttcttatgattttctc---tgttcagGGTATTGATGGCTCCAGAGTTGAAAAGGTGTTGGAATCTGTTCATATTGCAGCTAACAAGAACACCGTTCCTGGAGATGTGTCGGCCATGGTTCCTGGTG

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 12
-attatgtcagatcaataaaagaaagcagtgatttatttcattctaaagggtcagta-aaataggctaatcttttttttttttttcttttaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG
 | ||| | |||    |       |       | | | |  |  | ||   | | || ||| |||   | |  || ||| || |  ||||     ||| |||||||||||||||||||||||||| |||||||| ||| | |||||||||| |||||| |||||||||||||||||||||||||| |||||||||||| |||
aaatatttgagagttgttggctccatttaatttatgtgtattatttaacttttattataaaaaggaagagccattatttcttatgattttctc--tgttcagGGTATTGATGGCTCCAGAGTTGAAAAGGTGTTAGAATCTGTTCATATTGTAGCTAACAAAAACACTGTTCCTGGAGATGTGTCGGCCATGGTTCCTAGTG

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 12
attatgtcagatcaataaaag--aaagcagtgatttatttcattctaaagggtcagtaaaataggct-aatcttttttttttttttcttttaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG
  ||| ||   |  ||       | | ||    || ||   |||  |       |  |||  |   | |||  || ||       ||||| |    | |  ||||| | || ||||| ||||| |||   ||| ||||    | ||||||||| || || ||||||||||||||||||||||| |||||  | || ||||| |
-gtatttcctgtgcattccctctataacatcatttcatgctattgcagctttcgaagaaagaacattgaatagttattaacgaaatctttcatt--tttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAG

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|20813250|gb|BQ297728.1|BQ297728
EST:     TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|6134799|gb|AW133192.1|AW133192
EST:     TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTNCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|9900480|gb|BE609448.1|BE609448
EST:     TCTCTGGTGGAACCGAAAATCACCTGGTTTTGGTGAATCTGAAGAATAAT                         GGTATTGATGGCTCCAGAGTTGAGAAAGTGTTGGAAGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|120496684|gb|EH224851.1|EH224851
EST:     TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|9902305|gb|BE611273.1|BE611273
EST:     CTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: CTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|120496962|gb|EH225129.1|EH225129
EST:     TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|120532861|gb|EH260994.1|EH260994
EST:     TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|7326943|gb|AW620741.1|AW620741
EST:     TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|15203223|gb|BI425991.1|BI425991
EST:     TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|209699628|gb|BW655720.1|BW655720
EST:     TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|151399265|gb|EV269136.1|EV269136
EST:     TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|12690400|gb|BG156736.1|BG156736
EST:     CTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: CTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|151406194|gb|EV276009.1|EV276009
EST:     TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|22524932|gb|BU083743.1|BU083743
EST:     TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
EST: gi|209699198|gb|BW656187.1|BW656187
EST:     TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAGGCAGTTCATATTGCA
genomic: TCTCTGGTGGAACCGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagggtcagtaaaataggctaatcttttttttttttttcttttaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG
                      tctttttttttttttt  CT-rich tract
         taaaataggctaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attatgtcagatcaataaaagaaagcagtgatttatttcattctaaagggtcagtaaaataggctaatcttttttttttttttcttttaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - ttcattc