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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgttcttactgatttaagtaatttgatttgatttttgtttatgaagagaatggtgtggtgtgtggtttcaactaattgtgttgtgttgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG

Basic information

species Glycine max
transcript GLYMA01G25940.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G25940.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 3'ss of exon 1
gtattgttcttactgatttaagtaatttgatttgatttttgtttatgaagagaatggtgtggtgtgtggtttcaactaattgtgttgtgttgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG
                  |||||||||| |||   |   |    ||| ||||| |  | |  |   |  | |||  |   | ||| ||||   |  |||| ||||| ||||||||||||||||| |||||||| ||||| || |||||||| || || || ||| | || || ||||
-----------------gtaagtaattt-attcactagattcacatgcagagactcatattttcgatcttctcacatctctatgt-gtgtcacgagacagTCCTTCGGGAAAGCTTGTTCAGATCGAGCATGCATTGACCGCCGTTGGCTCAGGCCAAACATCTCTAGGGATCAAAG
















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|4397406|gb|AI496403.1|AI496403
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtattgttct ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
EST: gi|193466029|gb|FK429770.1|FK429770
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCTTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtattgttct ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
EST: gi|58014614|gb|CX701356.1|CX701356
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCNTTCTGGAAAGC-TGTTTCAGATTGAGCATGCC-TGNACAGCTGTTGGC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtattgttct ... tgtggaacagCCCTTCTGGAAAGCTTG-TTCAGATTGAGCATGCCTTG-ACAGCTGTTGGC
EST: gi|120494647|gb|EH222814.1|EH222814
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtattgttct ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
EST: gi|9564578|gb|BE474087.1|BE474087
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtattgttct ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
EST: gi|19052912|gb|BM731579.1|BM731579
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtattgttct ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
EST: gi|7925135|gb|AW831161.1|AW831161
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtattgttct ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
EST: gi|298198188|gb|HO039727.1|HO039727
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCCGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtattgttct ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
EST: gi|15204528|gb|BI427296.1|BI427296
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtattgttct ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
EST: gi|151406778|gb|EV276593.1|EV276593
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtattgttct ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
EST: gi|24206299|gb|BU965552.1|BU965552
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtattgttct ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagagaatggtgtggtgtgtggtttcaactaattgtgttgtgttgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG
                            aactaat  putative branch site (score: 2)
                            aactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgttcttactgatttaagtaatttgatttgatttttgtttatgaagagaatggtgtggtgtgtggtttcaactaattgtgttgtgttgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT