Sequence
atgc intronic sequence ATGC exonic sequencegtgagcataaaatgcaaatatatgattttcaagctttagtgatgcattattgttaaaatgacatgacttctaacctacaaactatatgccatttttgtgtgtccagTTCAACAAGGAAGTTGATAAGGTGATTGAGGAAATAAAGCTTAAGGTTGTTTATACAGTGCCTAGTGGAAGTTCCGACGACTCTGGTATTACATCTTTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g43594.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g43594.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 4
gtgagcataaaatgcaaatatatgattttcaagctt--tagtgatgcattattgttaaaatgacatgacttcta-acctacaaact---atatgccatt----tttgtgtgtccagTTCAACAAGGAAGTTGATAAGGTGATTGAGGAAATAAAGCTTAAGGTTGTTTATACAGTGCCTAGT---GGAAGTTCCGACGACTCTGGTATTACATCTTTAG
||||||| || |||| | | | || | | | || ||| | |||||||| || | ||| |||| || | | | ||| || ||| | || | |||| |||||||||||||||| ||||||||| || |||||||| ||||| |||||||| || ||| | ||||| ||| |||| || |||||| | | ||||||
gtgagcaagaagtgcaga-acaaatttgtaaggtttattagcgttgcattatccctatagtgaaatgatgtccacagccacacgctgctatacacggttacattacatgtgcgcagTTCAACAAGGAAGCTGATAAGGTAATCGAGGAAATGAAGCTCAAGGTTGTCTACACATTACCTAGCTGCGGAGGTTCAGATGACTCTAGCGTATCATCTT---
upper sequence: LOC_Os02g43594.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G171406_T05 (Zea mays), 3'ss of exon 2
gtgagcataaaatgcaaatatatgattttcaagctttagtgatgcattattgttaaaatgacatgacttcta-acctacaaact---atatgccatt----tttgtgtgtccagTTCAACAAGGAAGTTGATAAGGTGATTGAGGAAATAAAGCTTAAGGTTGTTTATACAGTGCCTAGT---GGAAGTTCCGACGACTCTGGTATTACATCTTTAG
| | || | |||| | |||||||| || | ||| |||| || | | | ||| || ||| | || | |||| |||||||||||||||| ||||||||| || |||||||| ||||| |||||||| || ||| | ||||| ||| |||| || |||||| | | ||||||
---------------------gtaaggttta----ttagcgttgcattatccctatagtgaaatgatgtccacagccacacgctgctatacacggttacattacatgtgcgcagTTCAACAAGGAAGCTGATAAGGTAATCGAGGAAATGAAGCTCAAGGTTGTCTACACATTACCTAGCTGCGGAGGTTCAGATGACTCTAGCGTATCATCTT--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttaaaatgacatgacttctaacctacaaactatatgccatttttgtgtgtccagTTCAACAAGGAAGTTGATAAGGTGATTGAGGAAATAAAGCTTAAGGTTGTTTATACAGTGCCTAGTGGAAGTTCCGACGACTCTGGTATTACATCTTTAG
ttctaac putative branch site (score: 1)
tttttgt putative PPT
aaactatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcataaaatgcaaatatatgattttcaagctttagtgatgcattattgttaaaatgacatgacttctaacctacaaactatatgccatttttgtgtgtccagTTCAACAAGGAAGTTGATAAGGTGATTGAGGAAATAAAGCTTAAGGTTGTTTATACAGTGCCTAGTGGAAGTTCCGACGACTCTGGTATTACATCTTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG