Sequence
atgc intronic sequence ATGC exonic sequence...atatttaatttctgatcatatgaatttcaagccctttagtttacatgttcttaatgattgaattcttctcctctttcctattttgtcttttttacttcagAATGTAGTGTTGTCTGGAGGTTCAACCATGTTCAAGGATTTTCACAGGAGGTTGCAACGTGATCTAAAAAAAATAGTGGATGCTCGTGTACTTTTATCTG
Basic information
species | Glycine max |
transcript | GLYMA08G13810.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 6
atatttaatttctgatcatatgaatttcaagccctttagtttacatgttcttaatgattgaattcttctcctctttcctattttgtctttt---ttacttcagAATGTAGTGTTGTCTGGAGGTTCAACCATGTTCAAGGATTTTCACAGGAGGTTGCAACGTGATCTAAAAAAAATAGTGGATGCTCGTGTACTTTTATCTG
||| || | | || | || | | ||| ||| | | || | | | | | | |||||||| |||||||||| ||||||||||| |||||||| ||||| || ||||| ||| | || || || || || || ||||||||||| ||| |
-----------------------gtttgaaacgccaaagactggtcagagttttaagataatttccaatccgcaatactgatgaatttgtgaaatcatttcagAATATAGTGTTGTCCGGAGGTTCAACTATGTTCAAAGATTTCGGAAGAAGGTTACAAAGGGACCTCAAGAAGATTGTTGATGCTCGTGTTCTTGCTAATA
upper sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 6
atatttaatttctgatcatatgaatttcaagccctttag-tttacatgttcttaatgattgaattcttc---tcctctttcctattttgtcttttttacttcagAATGTAGTGTTGTCTGGAGGTTCAACCATGTTCAAGGATTTTCACAGGAGGTTGCAACGTGATCTAAAAAAAATAGTGGATGCTCGTGTACTTTTATCTG
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ttcttcagtgttcagctgtattcatg--agtttactcagctttaattgctgtttatgtattcatgcatcaatctgtgtgtctgattttgacatttgt--ctcagAATATAGTTTTATCAGGAGGATCAACCATGTTCAAGGACTTCCACAGAAGGTTGCAGCGTGATGTAAAAAAAATTGTGGATGCTCGGGTTCTTGCTTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttcttaatgattgaattcttctcctctttcctattttgtcttttttacttcagAATGTAGTGTTGTCTGGAGGTTCAACCATGTTCAAGGATTTTCACAGGAGGTTGCAACGTGATCTAAAAAAAATAGTGGATGCTCGTGTACTTTTATCTG
tcttaat putative branch site (score: 3)
ttcttctcctctttcc putative PPT
tattttgtctttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatttaatttctgatcatatgaatttcaagccctttagtttacatgttcttaatgattgaattcttctcctctttcctattttgtcttttttacttcagAATGTAGTGTTGTCTGGAGGTTCAACCATGTTCAAGGATTTTCACAGGAGGTTGCAACGTGATCTAAAAAAAATAGTGGATGCTCGTGTACTTTTATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - -caagccc
- - - - - - - - - - - - - - - - - - - - - -catgttc