Sequence
atgc intronic sequence ATGC exonic sequence...cataaaatgtgaataagttctgtgatctcttgtgcttgccctgttatcgtaaatgctgtgactcttctgatttgttattttttcttttttttccctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG
Basic information
species | Glycine max |
transcript | GLYMA16G26220.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 8
cataaaatgtgaataagttctgtgatct--cttgtgcttgccctgtta-tcgtaaa----tgctgtgactcttctgatttgttattttttcttttt--tttccctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG
| | ||| |||| | | || | ||| || |||| || || | | | | || | |||| ||| || | | ||| |||| ||||| |||||||||||||| ||||| |||||||| ||| ||||||||||| |||||||||||||| ||||| ||| ||
---------ttgttgggttttgtggtttgctttttctttgattcattcctcgtgaacttgtgttttcatggtgctcagttgtaattgcttacataaaactattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG
upper sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 8
cataaaatgtgaataagttctgtgatctc--ttgtgcttgccctgttatcgtaaatgctgtgactcttctgatttgttattttttctt----ttttttccctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG
|||| |||| || | | || | || | | ||| ||| || || | || | | || || || |||| ||||| |||||||||||||||||||| |||||||| ||| ||||||||||| ||||||||||| || ||||| ||| ||
------atgttaatatatttcactggcacaaccttgttatttatggtgaaattaatatggtggtatctcaatttcttggttgtgaactgtaattattattgtgcagGTATTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTGTCTTTGTGGAGAGCATTCTTAGATATGGTCTGCCGCCATCATTCCTG
upper sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G128995_T01 (Zea mays), 3'ss of exon 8
---cataaaatgtgaataagttctgtgatctcttgtgcttgccctgttatcgtaaatgctgtgactcttctgatttgttattttttcttttttttccctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG
|||| || | | || | ||| || ||| | || | | || | |||| |||| | | | | || | | |||| ||||| |||||||||||||| ||||| |||||||| ||| |||||||| || ||||||||||| || ||||| ||| ||
gctttgttgctgtggttatatggtttgctgagttggtttttgccttctttctctttcg-tatgtcatttcttgcttgtgaactgtaactattactg--tacagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATCCTTAGATATGGTCTCCCTCCATCATTCCTG
upper sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 8
cataaaatgtgaataagttctgtgatctcttgtgcttgccctgttat-cgtaaatgctgtgactc----ttctgatttgttattttttctt-ttttttccctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG
| | | || |||| | || | || || | |||||| | | | | ||| | | | | | || |||| || |||||||||| |||||||||||||| || || ||||| ||||| ||||||||||| ||||| ||||| |||||||| ||| ||
------acgactccaccttgtgtggttggctgggtcaagtctcttttgcgtaaaagttccttcacaagggcctgttccttgaacggctgtaattatttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG
upper sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 8
cataaaatgtgaataagt-tctgtg-atctcttgtgcttgccctgttatcgtaaatgctgtgactcttctgatttgttattttttcttttttttccctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG
|| || ||| || || | | | | | |||| | | | | || |||| | | | | | ||| |||||||||||||||||||||| || ||||| |||||| ||| | ||||||||| ||||||| ||| | || || | ||||||
------------gtaggtatctacacattgctctgaatagatattctcttgtaa----tacaatacctg-aatctgttttgatcttcggtctacatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG
upper sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 8
cataaaatgtgaataagttctgtgatctcttgtgcttgccc--tgttatcgta----aatgctgtgactcttctgatttgttattttttcttttttttc-cctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG
||||||| | || ||| | | | | || | |||| | |||| | | ||| || || | || | |||| ||| |||||||||||||||||||||| |||||||| || ||||| ||| | ||||| || || |||||||| | |||||||| ||||||
-------tgtgaatgacttgtgttgttgatagagtgtggctattgttgtttccttccaatgttaaattttggtaattttatttttatatcatgagtttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcgtaaatgctgtgactcttctgatttgttattttttcttttttttccctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG
ttctgat putative branch site (score: 3)
ctcttctgatttgtta CT-rich tract
ttctgatttgttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cataaaatgtgaataagttctgtgatctcttgtgcttgccctgttatcgtaaatgctgtgactcttctgatttgttattttttcttttttttccctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - -ttctgtg
- - - - - - - - - - - - - -tcttgtg
- - - - - - - - - - - - - - - - - cttgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - gctgtga