Sequence
atgc intronic sequence ATGC exonic sequence...ttcaatttcattgtccaaaaaagatgttcaatatttctgaaaggaaattcttgttaattggaaaaagtttattcttaacaaatgtttcttctttgatcagTTTGCCCAACGACTCTGAAAAGGATATGCAGACAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTGAATCGATCATTGAAGAAGATACA
Basic information
species | Glycine max |
transcript | GLYMA13G42160.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G42160.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------------------ttcaatttcattgtccaaaaaagatgtt-----caatatttctgaaagga------aattc--ttgt-taattggaaaa--agttta-----ttcttaacaaatgtttcttctttgat-cagTTTGCCCAACGACTCTGAAAAGGATATGCAGACAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTGAATCGATCATTGAAGAAGATACA
| | || || | | ||| | |||| || | | ||| | |||| | || |||| | || ||| || || | || || | | | ||||||| || || || ||||||||||||||||||||||||||||| ||||||||||||| || ||||| || || || || ||||| | |||||||| ||
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
upper sequence: GLYMA13G42160.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G105004_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------ttcaatttcattgtccaaaaaagatgtt-caatatttctgaaaggaaattcttgttaat-------tggaaaaagtttattct--taacaaatgtttct--tctttgat-cagTTTGCCCAACGACTCTGAAAAGGATATGCAGACAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTGAATCGATCATTGAAGAAGATACA
| | | || | ||||| | | || || | ||| | | | | | | ||||| | | |||| | ||| || | | | | ||||||| |||||||| ||||| | ||||||||||||||||||||| | | |||||||| || ||||| || || || ||||| ||||||||||||||| |
gtgagccctactgtattgttacgaagtctctgttaaatctagatttgctgtgacattcacagtactgattactgaagataatgccatcattgtagaagaatttcttagattaggagattatggaatgaactgcttcttctgacacttgcctataaacaccattgcagTTTGTCCAACGACATTGAAACGAATATGCAGACAACATGGAATTTCCCGATGGCCATCTCGAAAGATAAACAAGGTCAATCGTTCATTGAAGAAGATAGA
upper sequence: GLYMA13G42160.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------ttcaat-ttcattgtccaaaaaagatgttcaatatttctgaaaggaaattctt--gttaattg-----gaaaaagtttattcttaacaaatgtttctt--ctttgat-cagTTTGCCCAACGACTCTGAAAAGGATATGCAGACAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTGAATCGATCATTGAAGAAGATACA
| | | |||| || | || | | || | | | ||| ||||| |||| || |||| || | | ||| || | | | | ||||||| ||||| ||| ||||| | ||||||||||||||||||||| | || |||||||| || ||||| || || || || || ||| |||||||||| |
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgc--agctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
upper sequence: GLYMA13G42160.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0094g00020.t01 (Vitis vinifera), 3'ss of exon 4
ttcaatttcattgtccaaaaaagatgttcaatatt-tctgaaaggaaattcttgttaattggaaaaagtttattcttaacaaatgtttcttctttgat---cagTTTGCCCAACGACTCTGAAAAGGATATGCAGACAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTGAATCGATCATTGAAGAAGATACA
| | || | | | | || || || | || ||| | | | | || || ||| | | || | ||| |||||| | |||||||||| || || || ||||| || |||||||||||||| || |||| ||||| ||||||||||| || || ||||| ||||| ||| |||||||||
agtagtcccaacaactagtataaata--agatgttatttggaagaagaagttggcaaactgtgt--agtctgatattgattttgattttatctttgttttacagTTTGCCCCACTACACTCAAAAGAATCTGCAGACAACATGGGATATCAAGATGGCCGTCCCGCAAGATCAACAAGGTGAACAGATCACTGAGGAAGATACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattcttgttaattggaaaaagtttattcttaacaaatgtttcttctttgatcagTTTGCCCAACGACTCTGAAAAGGATATGCAGACAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTGAATCGATCATTGAAGAAGATACA
tcttaac putative branch site (score: 2)
tttcttctttgatc putative PPT
aaaaagtttattctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaatttcattgtccaaaaaagatgttcaatatttctgaaaggaaattcttgttaattggaaaaagtttattcttaacaaatgtttcttctttgatcagTTTGCCCAACGACTCTGAAAAGGATATGCAGACAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTGAATCGATCATTGAAGAAGATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - aaaaaag
- - - - - - - - - - - - - - - - - - ctgaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaag