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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaccgtcatattgaaatattcatttgattcatctaacagatttctatttgtaaattgtctttcacagtttaactaatatgctctctgtctgtgatcagAGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTATTG

Basic information

species Glycine max
transcript GLYMA09G28470.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28470.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0130g00230.t01 (Vitis vinifera), 3'ss of exon 1
actaccgtcatattgaaatattcatttgattcatctaacagatttctatttgtaaattgtctttcacagttt---aactaatatgctctctgtc-tgtgat-cagAGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTATTG
           ||  | |   || | || |||||  ||    |||| || | |  |||  || |     |||    || ||| || || || || | | |  |||||| | |||||||||||||||||||| ||| |||| ||||||||||| || |||
----tttctggatccagaatatcttatgtttcatggaattcctttcaatatctctattccctgtttggattttctgaccaat-tgatccctctcatattacacagAGATTTTATGGTTTTGCCATATGCTTGGCTGCTGGTTTAACTTGTACACTCTTG
















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|192317985|gb|FK009465.1|FK009465
EST:     TCGCCTTCATGGACGACTTCAACCGCAACTGCACCTTGTCCACCACACAG                         AGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTA
genomic: TCGCCTTCATGGACGACTTCAACCGCAACTGCACCTTGTCCACCACACAGgtcatcacct ... ctgtgatcagAGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTA
EST: gi|298185755|gb|HO028066.1|HO028066
EST:     TCGCCTTCATGGACGACTTCAACCGCAACTGCACCTTGTCCACCACACAG                         AGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTA
genomic: TCGCCTTCATGGACGACTTCAACCGCAACTGCACCTTGTCCACCACACAGgtcatcacct ... ctgtgatcagAGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTA
EST: gi|192317986|gb|FK009466.1|FK009466
EST:     ATGGACGACTTCAACCGCAACTGCACCTTGTCCACCACACAG                         AGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTA
genomic: ATGGACGACTTCAACCGCAACTGCACCTTGTCCACCACACAGgtcatcacct ... ctgtgatcagAGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTA
EST: gi|298194667|gb|HO043139.1|HO043139
EST:     TCGCCTTCATGGACGACTTCAACCGCAACTGCACCTTGTCCACCACACAG                         AGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTA
genomic: TCGCCTTCATGGACGACTTCAACCGCAACTGCACCTTGTCCACCACACAGgtcatcacct ... ctgtgatcagAGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTA
EST: gi|7042065|gb|AW471959.1|AW471959
EST:     TCGCCTTCATGGACGACTTCAACCGCAACTGCACCTTGTCCACCACACAG                         AGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTA
genomic: TCGCCTTCATGGACGACTTCAACCGCAACTGCACCTTGTCCACCACACAGgtcatcacct ... ctgtgatcagAGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatttgtaaattgtctttcacagtttaactaatatgctctctgtctgtgatcagAGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTATTG
                           aactaat  putative branch site (score: 2)
                                     ctctctgtct  putative PPT
                      agtttaactaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaccgtcatattgaaatattcatttgattcatctaacagatttctatttgtaaattgtctttcacagtttaactaatatgctctctgtctgtgatcagAGACTATATGGTTTTGCCATATGCTTTGCTTCTGGATTAACTTGTACGCTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgctc