Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgactacgcgttatgttatacatctctctgatgcataccgtgtacctgattgaatatattgtaatttaccttgagtgaacattcagGTTGATGCCTATGAGGTAAAGAAGCAAGAGTTGATGCAAGAAAATGCTGATTTGCGAGCACTATTGCGTTCGATGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g14460.3 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G147500_T06 (Zea mays), 3'ss of exon 9
gtaagtgactacgcgttatgttatacatctctctgatgcataccgtgtacctgattgaatatattgtaatttaccttgagtgaacattcagGTTGATGCCTATGAGGTAAAGAAGCAAGAGTTGATGCAAGAAAATGCTGATTTGCGAGCACTATTGCGTTCGATGCAG
|| | | | | | | | | |||||||||| |||| | || || || || |||||||||||||| ||||| || ||||| |||||| |||||||||| ||||| ||||| || ||||| || ||||| ||||||
-------------------gtaagcagtaacgcaattttgaaatgcagatctgattgaatttattctgatgtatattatgt----attcagGTTGATGCATATGAAGTGAAGAAACAAGAGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAG
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 8
--------gtaagtgactac----gcgttatgttataca-tctctctgatgcataccgtgtacctgattgaatatattgtaatttaccttgagtgaacattcagGTTGATGCCTATGAGGTAAAGAAGCAAGAGTTGATGCAAGAAAATGCTGATTTGCGAGCACTATTGCGTTCGATGCAG
| | ||| || | || || || | | | | | | | |||||||||| |||| | || || || || |||||||||||||| ||||| || ||||| |||||| |||||||||| ||||| ||||| || ||||| || ||||| ||||||
aaaagaacgacaatgattattacaaaatgattgtaagcagtaacgcaattttgaaatgcagatctgattgaatttattctgatgtatattatgt----attcagGTTGATGCATATGAAGTGAAGAAACAAGAGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAG
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtgactacgcgttatgttatacatctctctgatgcataccgtgtacctgattgaatatattgtaatttaccttgagtgaacattcagGTTGATGCCTATGAGGTAAAGAAGCAAGAGTTGATGCAAGAAAATGCTGATTTGCGAGCACTATTGCGTTCGATGCAG
|||| || | || || || | ||| || || || || | ||||| ||||||||||||| ||| || |||||| ||||| ||||||| |||||||| | ||| |||| || || ||||||
---------------gtatgaagtatgattggcttattagagttttgattaacactgattaacttaagtgcgactatgtactgatgg-cagGTGGATGCCTATGAGGCAAAAAATCAAGAGCTGATGGCAGAAAATACTGATTTGAGGGCATTATTACGGTCAATGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcataccgtgtacctgattgaatatattgtaatttaccttgagtgaacattcagGTTGATGCCTATGAGGTAAAGAAGCAAGAGTTGATGCAAGAAAATGCTGATTTGCGAGCACTATTGCGTTCGATGCAG
acctgat putative branch site (score: 4)
tgattgaatatattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgactacgcgttatgttatacatctctctgatgcataccgtgtacctgattgaatatattgtaatttaccttgagtgaacattcagGTTGATGCCTATGAGGTAAAGAAGCAAGAGTTGATGCAAGAAAATGCTGATTTGCGAGCACTATTGCGTTCGATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT