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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgcactggtaaataatgggactgggaatctgtgttgtttaaattttgattggttttgggacttgttttcctgttatgataattctgtttttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCTGGGTGAG

Basic information

species Glycine max
transcript GLYMA13G31130.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 2
tcgcactggtaaataatgggactgggaatctgtgttgtttaaattttgattggt-tttgggacttgttttcctgttatgataattctgtttttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCTGGGTGAG
 | ||  |       |      |    || | |     | || | |    | ||  ||   |   | |   || || | ||  ||  || ||    ||||||||||||||||  ||||||||||||||||| |||||   ||| ||||| |||||||||
-ctcaaagtcctcccaaaatttttcttatttttacccataaagtatcatcttgtactttacagaggatcagcttttcttatttttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG
















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|208176390|gb|GD978597.1|GD978597
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|298182669|gb|HO031404.1|HO031404
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATACTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|193708153|gb|FK642459.1|FK642459
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|151407299|gb|EV277114.1|EV277114
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|41145367|gb|CK605578.1|CK605578
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|11413313|gb|BF425324.1|BF425324
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|298173823|gb|HO017159.1|HO017159
EST:     CCCACCACCGGTCGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|151403312|gb|EV273122.1|EV273122
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAACT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|298175030|gb|HO018025.1|HO018025
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGAGGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|298181172|gb|HO022611.1|HO022611
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|298190922|gb|HO038401.1|HO038401
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|17519909|gb|BM188951.1|BM188951
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|18040763|gb|BM309057.1|BM309057
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|8283060|gb|BE020621.1|BE020621
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|10846367|gb|BF071320.1|BF071320
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|192326806|gb|FK018558.1|FK018558
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
EST: gi|17400921|gb|BM177703.1|BM177703
EST:     CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT                         GCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT
genomic: CCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttc ... ttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattggttttgggacttgttttcctgttatgataattctgtttttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCTGGGTGAG
                                           ttttaat  putative branch site (score: 3)
                                     ttctgttttt  CT-rich tract
                            ttatgataattctgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgcactggtaaataatgggactgggaatctgtgttgtttaaattttgattggttttgggacttgttttcctgttatgataattctgtttttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCTGGGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - -atctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - -ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgtt