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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacttggttctttgatttcaattcttttttttcatttatagttcatgtcgatttatcccttctcccctaagctgataatagctccaattgtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGGTCCAAGCAAGTGGAAATAG

Basic information

species Glycine max
transcript GLYMA11G11950.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11950.3 (Glycine max), 3'ss of exon 2
lower sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgacttggttctttgatttcaattcttttttttcatttatagttcatgtcgatttatcccttctcccctaagctgataatagctccaattgtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGGTCCAAGCAAGTGGAAATAG
                       || ||||| || |  | | |   |  | ||  | |   ||  |   | |  |   | |   ||    |  | ||||||||||| ||||| ||||||||||| ||||| ||||||||||| ||||| ||||| || ||||| |||||||
----------------------gttgtttttcttaagcttttgactagtttgaagttttgatta-ctattgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG

upper sequence: GLYMA11G11950.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 2
gtgacttggttctttgatttcaattcttttttttcatttatagttcatgtcgatttatcccttctcccctaagctgataatagctccaattgtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGGTCCAAGCAAGTGGAAATAG
                 || ||       | || | | |||    |    |  | |||  |||||    ||| ||  |  ||  |||  || |      ||||||  |||||||||||||| || ||||| |||||||  || ||||| |||||||||||||| |||||||
----------------gttacacaatgcctcttacttctatgtaactgtcctgtatatttcttct----taacct--ttgtatatccttttctctcactagCATTTCCAAAGGGATATTGTCCGTGGTGTGGAAGGTTTCATAGTTACTGGGTCCAAGCAAGTTGAAATAG

upper sequence: GLYMA11G11950.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 2
gtgacttggttctttgatttcaattcttttttttcatttatagttcatgtcgatttatcccttctcccctaagctgataatagctccaattgtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGGTCCAAGCAAGTGGAAATAG
        |||  || ||      || | |  ||||||| |   |||     |||| |   || |  ||| | || |||| |  || |  |    |||||||||| |||||||||||||||||| ||||||||||||| ||| ||||| |||||||| ||||| |||||||
--------gttgcttaatcc----tcctgtggttcatttgtgactca-----atttgt---ttatttcctcaacttataa-atttctatatcatttttcagCATTTTCAAAGGGATATTGTTCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAG

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|298189490|gb|HO037893.1|HO037893
EST:     AGCTACACCAGAGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAG                         CATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
genomic: AGCTACACCAGAGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAGgtgacttggt ... gtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
EST: gi|298176009|gb|HO015414.1|HO015414
EST:     AACTACACCAGAGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAG                         CATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGCTATATTGTTACCGGG
genomic: AGCTACACCAGAGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAGgtgacttggt ... gtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
EST: gi|208270412|gb|GE067374.1|GE067374
EST:     AGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAG                         CATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
genomic: AGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAGgtgacttggt ... gtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
EST: gi|298180588|gb|HO025675.1|HO025675
EST:     AGCTACACCAGAGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAG                         CATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
genomic: AGCTACACCAGAGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAGgtgacttggt ... gtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
EST: gi|15285961|gb|BI469852.1|BI469852
EST:     GACTTGAGAAACTTTATATATCGACACGTGCGGGGAAG                         CATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
genomic: GACTTGAGAAACTTTATATATCGACACGTGCGGGGAAGgtgacttggt ... gtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
EST: gi|207713583|gb|GD695258.1|GD695258
EST:     CACCAGAGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAG                         CATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
genomic: CACCAGAGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAGgtgacttggt ... gtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
EST: gi|298173699|gb|HO017035.1|HO017035
EST:     AGCTACACCAGAGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAG                         CATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
genomic: AGCTACACCAGAGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAGgtgacttggt ... gtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
EST: gi|213599808|gb|DB968430.1|DB968430
EST:     AGCTACACCAGAGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAG                         CATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG
genomic: AGCTACACCAGAGACTTGAGAAACTTTATATATCGACACGTGCGGGGAAGgtgacttggt ... gtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcgatttatcccttctcccctaagctgataatagctccaattgtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGGTCCAAGCAAGTGGAAATAG
                         agctgat  putative branch site (score: 4)
                            tgataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacttggttctttgatttcaattcttttttttcatttatagttcatgtcgatttatcccttctcccctaagctgataatagctccaattgtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGGTCCAAGCAAGTGGAAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA