Sequence
atgc intronic sequence ATGC exonic sequence...catataaatattaaacaaagcatatgggatttttagtttttgagaacttaattatcctgtaggagcaaagactgacaatacttagcatttgaatttgaagCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
Basic information
species | Glycine max |
transcript | GLYMA16G08070.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G08070.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 4
catataaatattaaacaaagcatatgggatttttagtttttgagaacttaattatcctgtaggag-caaagactgacaatacttagcatttgaatttgaa-gCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
||| | || |||| || | | || || | | | || | | ||| ||| ||| ||||| | | | | |||||| |||||||||||||| |||| |||||||||||| | |||||||||||||| || |||| ||| | || |||||||| || ||||||||||| ||||||
-gtatttgaactactcaaaacaatc----tctatatcttcatggcattcaacgctgaaacatgagataaaaactaacaattacttgtgtcttgttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
upper sequence: GLYMA16G08070.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G21030.1 (Arabidopsis thaliana), 3'ss of exon 1
--catataaatattaaacaaagcatatgggatttttagtttttgagaacttaattatcctgtaggagcaaagactgacaatacttagcatttgaatttgaa-gCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
| ||| || | || | | | | || | || | | || | || | ||| ||| || || | | | | |||||| |||||||||||| ||||| |||||||||||| | ||||||||||||| || |||| ||| | || |||||||| || ||||||||||| ||||||
gtattttaactactcaaaacaatctctatatcttcatgacattcaaagctggaacat------gagataaaaactaaccattacttgtgtcttgttttgaaagCCGAGAGATGTACAATAAGTGGCAAGCTCAACGGCGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
upper sequence: GLYMA16G08070.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0033g00590.t01 (Vitis vinifera), 3'ss of exon 2
catataaatattaaacaaagcatatgggatttttagtttttgagaacttaattat-cctgtaggagcaaagactga--caatacttagcattt-gaatttgaagCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
| ||| |||| | | |||| | | || | || | | | | | | | | ||| | | || | ||| |||||||||||| |||||||||||||||||||||||||| |||||||||| |||||||| ||| | |||||||| || ||||| ||||||||||| || ||||||
---tttcatag-aaactgggactttggggcctcaatttgcttgaaatatcttgagattttttgttgtggaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttaattatcctgtaggagcaaagactgacaatacttagcatttgaatttgaagCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
gactgac putative branch site (score: 2)
atttgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catataaatattaaacaaagcatatgggatttttagtttttgagaacttaattatcctgtaggagcaaagactgacaatacttagcatttgaatttgaagCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - aaacaaa
- - - - - - - - - -gcatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgaca