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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttacacaatgtgattgtgtggatccaaatatctcttttatgtccctatttcaagtgaaaaggttaattactgtctattttggatttaatgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCTACAGCAGTTGTACTTCAG

Basic information

species Glycine max
transcript GLYMA10G36600.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G36600.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 12
agttacacaatgtgattgtgtggatccaaatatctcttt-tatgtccctat--ttcaagtgaaaaggttaattactgtctattttggatttaatgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCTACAGCAGTTGTACTTCAG
   ||    ||    |||| |   |     ||||  | |  ||||   |     | |  ||||||  |   |   || | ||  |  ||  ||   ||||||||| ||||||||  |||||||||| |||||||| |||||  |||||||||||||||||||||| ||||||
-tgtattggatccatttgtctttttttttttatcattgtgcatgtttgtgcaacttacatgaaaatttctctgcgtgacgatcct--atccaaatgtatgtagGTGGTTGATGCGCTATGCAACGTCGTATCAGCATCACCGGCAAAAGCAGCTACAGCAGTTGTTCTTCAG
















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|9564453|gb|BE473962.1|BE473962
EST:     AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAG                         GTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
genomic: AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAGgtacaagcac ... tgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
EST: gi|9903260|gb|BE612228.1|BE612228
EST:     AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAG                         GTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
genomic: AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAGgtacaagcac ... tgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
EST: gi|112361173|gb|EE400151.1|EE400151
EST:     AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAG                         GTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
genomic: AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAGgtacaagcac ... tgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
EST: gi|19348200|gb|BM892732.1|BM892732
EST:     AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAG                         GTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
genomic: AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAGgtacaagcac ... tgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
EST: gi|151406577|gb|EV276392.1|EV276392
EST:     AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAG                         GTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
genomic: AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAGgtacaagcac ... tgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
EST: gi|11687896|gb|BF595572.1|BF595572
EST:     AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAG                         GTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
genomic: AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAGgtacaagcac ... tgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
EST: gi|22524291|gb|BU083102.1|BU083102
EST:     CTGCCCAATAGGGCTGGAGACAG                         GTTGTTGATGCATTATGCAATGTTGTGTCAGCCTCACCAACAAAAGCAGCT
genomic: CTGCCCAACAGGGCTGGAGACAGgtacaagcac ... tgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
EST: gi|15200260|gb|BI424257.1|BI424257
EST:     AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAG                         GTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
genomic: AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAGgtacaagcac ... tgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
EST: gi|33390206|gb|CA853413.1|CA853413
EST:     AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAG                         GTTGTTGATGCATTATGCA
genomic: AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAGgtacaagcac ... tgttatgtagGTTGTTGATGCATTATGCA
EST: gi|9902661|gb|BE611550.1|BE611550
EST:     AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAG                         GTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT
genomic: AAACACAACCTTGTGCAGAAAGCACTTCTGCCCAACAGGGCTGGAGACAGgtacaagcac ... tgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatttcaagtgaaaaggttaattactgtctattttggatttaatgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCTACAGCAGTTGTACTTCAG
                                       atttaat  putative branch site (score: 4)
                               tattttggatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttacacaatgtgattgtgtggatccaaatatctcttttatgtccctatttcaagtgaaaaggttaattactgtctattttggatttaatgttatgtagGTTGTTGATGCATTATGCAACGTTGTATCAGCCTCACCAACAAAAGCAGCTACAGCAGTTGTACTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT