Sequence
atgc intronic sequence ATGC exonic sequence...cagtttggtttgtttgtttttttcacacccctagcatgtggtaatttaagtttgatttttccattgattgtggctctttatttttattttttggctgcagGGAAAGATTGTTTTTGTCTTATGCCAACTGGAGGAGGCAAGTCGATGTGTTATCAGATCCCTGCATTGGCAAAAGCAGGCATTGTGCTTGTCGTTTGCCC
Basic information
species | Glycine max |
transcript | GLYMA09G08180.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G08180.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G039683_T01 (Zea mays), 3'ss of exon 2
------cagtttggtttgtttgttt-ttttcacacccctagcatgtggtaatttaagttt----gatttttcca-----ttgattgtggctctttatttttattttttggctgcagGGAAAGATTGTTTTTGTCTTATGCCAACTGGAGGAGGCAAGTCGATGTGTTATCAGATCCCTGCATTGGCAAAAGCAGGCATTGTGCTTGTCGTTTGCCC
| ||| | | | || | || | | | | || || | | | ||| ||| ||| || | | || || | | || || ||| |||||||| |||||| |||||| | ||||||||||| || || ||||| ||||| |||||||| || || ||| ||| |||||||||| |||||| ||| ||
gtctgctcgcttgctgcgctcgtgtgttcttatatctgtaattggttggcacctgtgttgctgagatgttttcaacgtatgggttttgtttaatatgttatacaatttatgtgcagGGAGAGATTGCTTTTGTTTGATGCCAACTGGTGGTGGAAAGTCCATGTGCTATCAGATTCCAGCTCTGGTGAAAACAGGCATTGTTCTTGTCATTTCACC
upper sequence: GLYMA09G08180.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G35740.1 (Arabidopsis thaliana), 3'ss of exon 1
cagtttggtttgtttgtttttttcacacccctagcatgtggtaatttaagtttgatttttccattgattgtggctctttatttttattttttggctgcagGGAAAGATTGTTTTTGTCTTATGCCAACTGGAGGAGGCAAGTCGATGTGTTATCAGATCCCTGCATTGGCAAAAGCAGGCATTGTGCTTGTCGTTTGCCC
| | || |||| | | || | | || ||| | |||| || | ||| |||| | || | ||| | | | ||| | ||||| ||||| | |||||||| |||||||| || ||||| ||||||||||| |||||||| || ||| | || || || ||||| || | ||
--------gtaagtcgtaattttt-ctcttttactccggagaaaattagaat-gattgttttag-aatt----ctctgttttgtgattgatgagat-tagGAAGGGATTGCTTTTGCTTGATGCCAACGGGAGGAGGAAAATCGATTTGTTATCAGATACCTGCATTAGCTAAACCTGGAATCGTCCTTGTTGTGTCTCC
upper sequence: GLYMA09G08180.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g00850.t01 (Vitis vinifera), 3'ss of exon 1
----cagtttggtttgtttgtttttttcacacccctagcatgtggtaatttaagtttgatttttccattgattgtggctctttatttttattttttggctgcagGGAAAGATTGTTTTTGTCTTATGCCAACTGGAGGAGGCAAGTCGATGTGTTATCAGATCCCTGCATTGGCAAAAGCAGGCATTGTGCTTGTCGTTTGCCC
||| | | ||| | || | ||| | ||| | ||| ||| | | ||| | | | ||| | || |||| |||||| | ||||||||||||||| |||||||| |||||||| ||||| |||||||||||||| |||||| |||||||| |||| |||||||| || ||||| ||
cagtcagaaagagtgtagagttatgttggcgatcctt-tgtatggaatttt---tttaaacagtgatttgggttctgttgattagtgctaattttcttgtgcagGAAGAGATTGTTTTTGTCTCATGCCAACAGGAGGAGGAAAGTCAATGTGTTATCAGATTCCTGCACTGGCAAAACCAGGGATTGTGCTCGTGGTTTGTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagtttgatttttccattgattgtggctctttatttttattttttggctgcagGGAAAGATTGTTTTTGTCTTATGCCAACTGGAGGAGGCAAGTCGATGTGTTATCAGATCCCTGCATTGGCAAAAGCAGGCATTGTGCTTGTCGTTTGCCC
cattgat putative branch site (score: 4)
ctctttatttttattt putative PPT
tctttatttttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagtttggtttgtttgtttttttcacacccctagcatgtggtaatttaagtttgatttttccattgattgtggctctttatttttattttttggctgcagGGAAAGATTGTTTTTGTCTTATGCCAACTGGAGGAGGCAAGTCGATGTGTTATCAGATCCCTGCATTGGCAAAAGCAGGCATTGTGCTTGTCGTTTGCCC
- - - - - tgtttgt
- - - - - - - - - - - tcacacc
- - - - - - - - - - - - - - - - -gcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattgtg