Sequence
atgc intronic sequence ATGC exonic sequence...gtaccatgctaatgatatctatgcataggttgttaataggaacactgccacaaataaagggatcagccctttaattttttttttctggtcattttggtagATTGCTACTTCACTTTGAAGGCGTGGAATGCACAGAATGGTGGAGCAGCAGCTATTCTTGTAGCTGATGACAAGGCAGAAACGTTGATCACTATGGACAC
Basic information
species | Glycine max |
transcript | GLYMA09G41070.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G41070.3 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 1
gtaccatgctaatgatatctatgcataggttgttaataggaacactgccac--aaataaagggatcagccctttaattttttttttctggtcattttggta----gATTGCTACTTCACTTTGAAGGCGTGGAATGCACAGAATGGTGGAGCAGCAGCTATTCTTGTAGCTGATGACAAGGCAGAAACGTTGATCACTATGGACAC
| ||| ||| | ||||| | | | | | || | || | || || | ||| || | | ||||| | | ||| ||||||| ||||| |||||| ||||||||||| || | |||||||||||| || ||||| |||||||||||| | ||| | |||| || ||||||||
--attatg-taacact-tctatttgtcttctctctaatgtctcattcttacttgattacctaaatatacagtttg--ttatgtgacatggtctctgttgtatacagATTGCTTTTTCACAAAGAAGGCATGGAATGCACAAAACGCTGGAGCAGCAGCCATCCTTGTTGCTGATGACAAGACGGAACCCCTGATTACAATGGACAC
upper sequence: GLYMA09G41070.3 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 1
-----gtaccatgctaatgatatctatgcataggttgttaataggaacactgccac--aaataaagggatcagccctttaattttttttttctggtcattttggtagATTGCTACTTCACTTTGAAGGCGTGGAATGCACAGAATGGTGGAGCAGCAGCTATTCTTGTAGCTGATGACAAGGCAGAAACGTTGATCACTATGGACAC
||| ||| || | ||| | | | || || || ||||| | | | | | | | | | | | | || || |||||||| ||||| |||||| ||||||||||| || | ||||||||||| || ||||| |||||||||||| | ||| | |||| || ||||||||
attatgtaacatttctatt-tgtcttctctctaatgtctcattcttacttgattacctaaatataaagttt-gttatgtgacatggtctctgttgt-at----acagATTGCTTTTTCACAAAGAAGGCATGGAATGCACAAAACGCAGGAGCAGCAGCCATCCTTGTTGCTGATGACAAGACTGAACCCCTGATTACAATGGACAC
upper sequence: GLYMA09G41070.3 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 2
gtacca-tgctaatgatatctatgcataggttgttaataggaacactgccacaaataaagggatcagccctttaattttttttttctggtcatt-ttggtagATTGCTACTTCACTTTGAAGGCGTGGAATGCACAGAATGGTGGAGCAGCAGCTATTCTTGTAGCTGATGACAAGGCAGAAACGTTGATCACTATGGACAC
|| | | || | | | | || | |||| | ||| || | | | | || ||| | | | || || | || || |||||||||||| | |||||| |||||||||||||| | ||||||||||| || ||||| ||||||||||| | ||| | | || || |||||||
-taaaactccttccggtctgttctcagatgttgc-atcaggttcattaaaatagacaatgggtatgcatatagcaatacaattcaatgtttgttgtttacagATTGCTACTTTGCAAAGAAGGCATGGAATGCACAGAAAGCAGGAGCAGCAGCAATCCTTGTCGCTGATGACAAAGATGAACCTCTAATTACAATGGACAA
upper sequence: GLYMA09G41070.3 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 1
------gtaccatgctaatgatatctatgcataggttgttaataggaacactgccacaaataaagggatcagccctttaattttttttttctggtcattttggtagATTGCTACTTCACTTTGAAGGCGTGGAATGCACAGAATGGTGGAGCAGCAGCTATTCTTGTAGCTGATGACAAGGCAGAAACGTTGATCACTATGGACAC
| | | | || ||| |||| ||| | || | | | |||| | | || | | ||| | | | | | || ||| |||||| |||||| | |||||| |||||||||||||| | |||||||| || || ||||| ||||||||||| | ||| | | || || |||||||
ctgtctgctctcagatgttgcatcctactactagg--gttcactaaaata-tactacaacggactgcat-attaatacaatatactgtctgttgttgttt--acagATTGTTACTTCGCAAAGAAGGCATGGAATGCACAGAAAGCAGGAGCAGCGGCAATCCTTGTTGCTGATGACAAAGACGAACCTCTAATTACAATGGACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgccacaaataaagggatcagccctttaattttttttttctggtcattttggtagATTGCTACTTCACTTTGAAGGCGTGGAATGCACAGAATGGTGGAGCAGCAGCTATTCTTGTAGCTGATGACAAGGCAGAAACGTTGATCACTATGGACAC
ctttaat putative branch site (score: 4)
ttttttttttctggtc CT-rich tract
tttaattttttttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccatgctaatgatatctatgcataggttgttaataggaacactgccacaaataaagggatcagccctttaattttttttttctggtcattttggtagATTGCTACTTCACTTTGAAGGCGTGGAATGCACAGAATGGTGGAGCAGCAGCTATTCTTGTAGCTGATGACAAGGCAGAAACGTTGATCACTATGGACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- -ccatgct
- - - - - - - - - ctatgca
- - - - - - - - - - - - - -ggttgtt
- - - - - - - - - - - - - - - - - - - - - cactgcc
- - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa