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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacaattccaccttcttctttcaattttgagttctttttttctttatatctaactcgataatgggattttgattgcttcaaattctgttgaaattttaattttccgaaacaaattaaacagtgcaaaagtaggtaatagtgtctgctaaatgtatttatgtgctcattaattaatctctatttcatgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCTGAAGAAATTGGTTTTACTCATCAGGGGAGTCTAGGTCCAACTTATGGCG

Basic information

species Glycine max
transcript GLYMA10G38530.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G38530.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0022g02410.t01 (Vitis vinifera), 3'ss of exon 1
gttacaattccaccttcttctttcaattttgagttctttttttctttatatctaactcgataatgggattttgattgcttcaaattctgttgaaattttaattttccgaaacaaattaaac-agtgcaaaagtaggtaatagtgtctgctaaatgtatttatgtgctcattaattaatctctatttcatgt-tttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCTGAAGAAATTGGTTTTACTCATCAGGGGAGTCTAGGTCCAACTTATGGCG
                                                                                                  |   ||| ||||    ||  ||  | ||      |    || |   |||  |  |  ||||   ||  | ||   ||   || | ||| |  | ||||||| || ||||| ||| | || ||||||||||||||||||||||| |||||||||  ||| ||||| || || || || ||||| || |||||  | ||||
-------------------------------------------------------------------------------------------------atgccttttcgaacttgatagaaggaatgatttcttcttaaacacattcttattgagttattctggtcataatagtttctactttgtttaagatgtttagGTGCAAAATTTCTTCACGTCTGCTGAATCAAAGGCATTCGTTAAGATTGCTGAATCAATGGGTTTCACCCACCAAGGAAGTCTTGGCCCAACGAAAGGCG
















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|298195506|gb|HO043897.1|HO043897
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|298169244|gb|HO020604.1|HO020604
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|298176003|gb|HO015408.1|HO015408
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|298188227|gb|HO034920.1|HO034920
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGTGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|298190800|gb|HO032921.1|HO032921
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|298186419|gb|HO037052.1|HO037052
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|192331818|gb|FK024922.1|FK024922
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|298177788|gb|HO027341.1|HO027341
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|151404381|gb|EV274191.1|EV274191
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|298180216|gb|HO025431.1|HO025431
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAGATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|192301620|gb|FG998472.1|FG998472
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|192330573|gb|FK022704.1|FK022704
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|298175541|gb|HO018252.1|HO018252
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTGTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|192316313|gb|FK011672.1|FK011672
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|37997497|gb|CF809086.1|CF809086
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
EST: gi|192310334|gb|FK002214.1|FK002214
EST:     CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACG                         GTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT
genomic: CCAAAAAGAATCTTCAGATTAGCCGCCTCCGAGATTTCGATCTCTTCACGgttacaattc ... catgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtctgctaaatgtatttatgtgctcattaattaatctctatttcatgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCTGAAGAAATTGGTTTTACTCATCAGGGGAGTCTAGGTCCAACTTATGGCG
                                    tctctatttc  CT-rich tract
                           attaattaatctctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacaattccaccttcttctttcaattttgagttctttttttctttatatctaactcgataatgggattttgattgcttcaaattctgttgaaattttaattttccgaaacaaattaaacagtgcaaaagtaggtaatagtgtctgctaaatgtatttatgtgctcattaattaatctctatttcatgttttagGTCCAGAATTTTTTCTCCTCCGCTGAATCAAAGGCATTCGTTAAAATTGCTGAAGAAATTGGTTTTACTCATCAGGGGAGTCTAGGTCCAACTTATGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA