Sequence
atgc intronic sequence ATGC exonic sequence...gaaagctttagaaccaaaaaagggaaaggaaatgacctcactgtatttgaaattagccttgttttacacttattttctttttcttttctttttgtatcagTTATTGCGAGTGCTTTGCTGCTGGTGTCTACTGCATAGAACCCTGCTCCTGTCAGGATTGCTTCAACAAACCTATTCATGAAGACACTGTTCTTCAAACT
Basic information
species | Glycine max |
transcript | GLYMA01G44670.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 5
lower sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 4
gaaagctttagaaccaaaaaagggaaaggaaatgacctcactgtatttgaaattagccttgttttacacttattttctttttcttttctttttgtatcagTTATTGCGAGTGCTTTGCTGCTGGTGTCTACTGCATAGAACCCTGCTCCTGTCAGGATTGCTTCAACAAACCTATTCATGAAGACACTGTTCTTCAAACT
| ||||| | | | | ||| || | || ||| || | || || |||| | | || | | || |||||| || || |||||||||||||| ||||| |||||||| || || || ||| || |||||||| |||||||| ||||||||| ||| || |||
gtaagctccaaagttccacatttt--------tgatctt-tggcccttcaaaaaagtttggtgttttgag-----tcttctgatgtttgtgtggtg-cagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT
upper sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 5
gaaagctt-tagaaccaaaaaagggaaaggaaatgacctcactgtatttgaaattagccttgttttacacttatt-----ttctttttcttttctttttgtat-cagTTATTGCGAGTGCTTTGCTGCTGGTGTCTACTGCATAGAACCCTGCTCCTGTCAGGATTGCTTCAACAAACCTATTCATGAAGACACTGTTCTTCAAACT
| ||||| || || | | |||| | | ||| | ||| || | | || || ||| || ||| | | | |||||| || || |||||||||||||| || || |||||||| || || || ||| |||||||||||||||||||| |||||||| |||||| | ||
gtaagctcataccccctagcatctcgttaattcctacctgttcaaaataaaaaactgaattgccttgaagtagttaaccattgtttgactcccttttctttctgcagTTACTGTGAATGCTTTGCTGCTGGGGTTTATTGCATAGAGCCATGTTCATGTATAGATTGCTTCAACAAACCTATCCATGAAGAAACTGTTTTGGCTACC
upper sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
gaaagctttagaaccaaaaaagggaaaggaaatgacctcactgtatttgaaattagccttgttttacacttat--tttctttttcttttctttttgtatcagTTATTGCGAGTGCTTTGCTGCTGGTGTCTACTGCATAGAACCCTGCTCCTGTCAGGATTGCTTCAACAAACCTATTCATGAAGACACTGTTCTTCAAACT
|||| | | | ||| | | | | | || | || |||||| ||||| ||| || | ||| || |||||| || || ||||||||||||||||||||||| |||| || || || || || || ||||| |||||||||||||||||||| ||||||||| ||||
--tgtctttgaatctttgaggggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgaaattagccttgttttacacttattttctttttcttttctttttgtatcagTTATTGCGAGTGCTTTGCTGCTGGTGTCTACTGCATAGAACCCTGCTCCTGTCAGGATTGCTTCAACAAACCTATTCATGAAGACACTGTTCTTCAAACT
ccttgttttacactta CT-rich tract
ttattttctttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaagctttagaaccaaaaaagggaaaggaaatgacctcactgtatttgaaattagccttgttttacacttattttctttttcttttctttttgtatcagTTATTGCGAGTGCTTTGCTGCTGGTGTCTACTGCATAGAACCCTGCTCCTGTCAGGATTGCTTCAACAAACCTATTCATGAAGACACTGTTCTTCAAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA