Sequence
atgc intronic sequence ATGC exonic sequence...cattttccagtgtacactctttgatttttcctatttctttgctataatattttttttattaatggaaaattctgaaaacaaattaaatcatattggccagGTGGTCTCAAATAGCACAGCATTTGCCAGGAAGGACTGACAATGAGATAAAAAATTATTGGCATTCATATTTGAAAAAGAAAGAGATCAAAGCCAAGGAA
Basic information
species | Glycine max |
transcript | GLYMA16G31280.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G31280.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G25560.1 (Arabidopsis thaliana), 3'ss of exon 2
cattttccagtgtacactctttgatttt-tcctatttctttgctataatattttttttattaatggaaaattctgaaaacaaattaaatcatattggccagGTGGTCTCAAATAGCACAGCATTTGCCAGGAAGGACTGACAATGAGATAAAAAATTATTGGCATTCATATTTGAAAAAGAAAGAGATCAAAGCCAAGGAA
|||||| |||| || | |||||| ||| | | | || | || || | || | ||| | ||| |||||||| |||||||| | || || ||||| || |||||||||||||| || |||||||| || |||||||||||||| | |||| | ||
-----gtaagtgtat-ctctaagacctaaccctattgttttagcaga-------tgctagttatagagagact----aatgatttaggtgtaatt----agGTGGTCGCAAATAGCTAAATTCTTACCGGGAAGAACAGACAATGAGATAAAGAACTATTGGCACTCTCATTTGAAAAAGAAATGGCTCAAGTCTCAGAGC
upper sequence: GLYMA16G31280.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g00050.t01 (Vitis vinifera), 3'ss of exon 2
cattttccagtgtacactctttgatttttcctatttctttgctata-atattttttttatta-atggaaaattctgaaaacaaattaaatcatattggccagGTGGTCTCAAATAGCACAGCATTTGCCAGGAAGGACTGACAATGAGATAAAAAATTATTGGCATTCATATTTGAAAAAGAAAGAGATCAAAGCCAAGGAA
| || ||| ||| | ||| ||| | | | || || || | || || |||| |||| | | | |||| |||||||||||| ||||| ||| |||| || ||||| ||||| |||||||| || || || |||||||||| | | || ||||||| | | ||||| |||||
-gggacagaaactattctccatgagaaactcaatt-cttggttgtggatgttccttattttgtattgaaatgattgaatttatcaatattttcattgatcagGTGGTCTCAGATAGCGCAGAATTTTCCTGGAAGAACTGATAATGAGATTAAGAACTACTGGCATTCATGTCTCAAGAAGAAAGTGGTGAAAGCTCAGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatattttttttattaatggaaaattctgaaaacaaattaaatcatattggccagGTGGTCTCAAATAGCACAGCATTTGCCAGGAAGGACTGACAATGAGATAAAAAATTATTGGCATTCATATTTGAAAAAGAAAGAGATCAAAGCCAAGGAA
tattaat putative branch site (score: 2)
tttttttattaatgga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattttccagtgtacactctttgatttttcctatttctttgctataatattttttttattaatggaaaattctgaaaacaaattaaatcatattggccagGTGGTCTCAAATAGCACAGCATTTGCCAGGAAGGACTGACAATGAGATAAAAAATTATTGGCATTCATATTTGAAAAAGAAAGAGATCAAAGCCAAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - -tccagtg
- - - - - - tacactc
- - - - - - - - - - - - - - - - - - - -tgctata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa