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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattatattttggtttgatttgatgattgcctagatagttgtattattgttatttttgctttctatgaggttctttaatgataaaatctgtgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAAAGGCCAGACTCTCGATGACCTGAGTGAGGCTTTACTGGAAGATTGTGCT

Basic information

species Glycine max
transcript GLYMA06G08640.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G08640.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0008g03810.t01 (Vitis vinifera), 3'ss of exon 1
cattatattttggtttgatttgatgattgcctagatagttgtattatt--gtt--atttttgctttctatgaggttctttaatgataaaatctgtgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAAAGGCCAGACTCTCGATGACCTGAGTGAGGCTTTACTGGAAGATTGTGCT
| || |||||| | ||| ||| ||| | || | || || ||| || ||| ||||| | | | ||| | | | ||| | ||||| ||||| ||||| ||||| ||||||||||| ||||| || ||||||| || ||||| | ||||| | ||||| | ||||||||| |||||||||
---ttctcttaagtttgaatc-atgcatgcttagttttttttttttttcagttccatgttttctttcagtcaaagagcgttatggaagggcttatttatcgcagGTTTCATGTGGATAAGATGTCCTCAGCCCATGTTTATGTAAGATTGCACAAGGGTCAGACAATTGATGATATAAGTGAAGGTTTACTGGAGGATTGTGCT
















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|120534483|gb|EH262616.1|EH262616
EST:     AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
genomic: AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
EST: gi|298183696|gb|HO028909.1|HO028909
EST:     AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
genomic: AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
EST: gi|298164673|gb|HO014318.1|HO014318
EST:     AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
EST: gi|298173543|gb|HO016879.1|HO016879
EST:     AAGTTCGAGAACGAGGGACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
genomic: AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
EST: gi|151411303|gb|EV281114.1|EV281114
EST:     GGTTTTCCCGAAGACATCTG                         GTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
genomic: GGTTTTCCCGAAGACATCTGgtaaccctaa ... tgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
EST: gi|151412239|gb|EV282051.1|EV282051
EST:     AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTTGATAAAATGTCTTCAGCCCACGTCTATGTCAGGCTGCACAA
genomic: AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
EST: gi|6455553|gb|AW186236.1|AW186236
EST:     AAGT-CGAGAACTAGGACCTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
genomic: AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
EST: gi|58016161|gb|CX702903.1|CX702903
EST:     AAGTTCGAGANCGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATG-TGATAAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACA
genomic: AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tgtattgtagGTTCCATGTTGAT-AAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACA
EST: gi|151394766|gb|EV264637.1|EV264637
EST:     AGGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
genomic: AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
EST: gi|58015274|gb|CX702016.1|CX702016
EST:     AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
genomic: AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
EST: gi|18734019|gb|BM527940.1|BM527940
EST:     AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
genomic: AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
EST: gi|298168083|gb|HO013346.1|HO013346
EST:     AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA
genomic: AAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttatttttgctttctatgaggttctttaatgataaaatctgtgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAAAGGCCAGACTCTCGATGACCTGAGTGAGGCTTTACTGGAAGATTGTGCT
                           ctttaat  putative branch site (score: 4)
 ttctttaatgataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattatattttggtttgatttgatgattgcctagatagttgtattattgttatttttgctttctatgaggttctttaatgataaaatctgtgtattgtagGTTCCATGTTGATAAAATGTCTTCAGCCCATGTCTATGTCAGGCTGCACAAAGGCCAGACTCTCGATGACCTGAGTGAGGCTTTACTGGAAGATTGTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - -tgatttg
- - - - - - - - - - - -tgattgc