Sequence
atgc intronic sequence ATGC exonic sequence...atcggaataaatctcttgatgtttagaatgagattcggtcaaaatccgcctcatgcacctaagtctgactaagtggttgactgatcattggtgcgtgtagGAGGAAGGATGGGTGGTCTGCCGGGTGTTCAAGAAGCGGGTGGCGACGGTGCGGAGAATGGCCGACGGATCACCGTGCTGGTTCGATGACCACGGCGCCG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g42970.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g42970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G354151_T01 (Zea mays), 3'ss of exon 4
atcggaataaatctcttgatgtttagaatgagattcggtcaaaatccgcctcatgcacctaagtctgac--taagtggttgactga-tcattgg---tgc-gtgtagGAGGAAGGATGGGTGGTCTGCCGGGTGTTCA-AGAAGCGGGTGGCGACGGTGCGGAGAATGGCCGACGGATCACCGTGCTGGTTCGATGACCACGGCGCCG-----
||| || | | || ||| || | | | || | | ||| || || | || | || |||| | ||| | || || | | | || || | | || | |||| ||| | ||| || |||| | || | | || | | |
------gtaagcctgccgccctgcctgatccgatacgtacgatccctagctagttagc--aagctgaacaacaaatcgtccatcgagtcatcgagcatgccattcagctcagCTGACGACAGCATTTCCTCCTGCTTGCACGTACGTACGTGGACGATGCACGAATTGGTCG-TTCATCAGGAGGAAGGATGGGTGGTCTGCAGGGTGTTCAT
upper sequence: LOC_Os02g42970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G315140_T01 (Zea mays), 3'ss of exon 3
--atcggaataaatct-cttgatgtttagaatgagattcggtc---aaaatccgcctcatgcacctaagtctgactaagtg--gttgactgatcattggtgcgtgtagGAGGAAGGATGGGTGGTCTGCCGGGTGTTCAAGAAGCGGGTGGCGACGGTGCGGAGAATGGCCGACGGATCACCGTGCTGGTTCGATGACCACGGCGCCG---
| | || ||||||| ||| | | | || | || | ||| || | | || | |||| | | | ||| | || ||||||||||||||||||| ||| |||||||||||||||| |||||||| |||||||| ||||||||||| | ||| ||||| || |||||| |||||
gtacgtaagcttgcctgcttgatgcctagctgaacaacagatctcgagcatgccattcaggctgacagcatttgcttcttcctgttgcccgtcgaatggcg-gttcagGAGGAAGGATGGGTGGTGTGCAGGGTGTTCAAGAAGCGAGTGGCGACCGTGCGGAGGATGGCCGACGGCGCGCCG---TGGTTTGACAACCACGTCGCCGGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgcctcatgcacctaagtctgactaagtggttgactgatcattggtgcgtgtagGAGGAAGGATGGGTGGTCTGCCGGGTGTTCAAGAAGCGGGTGGCGACGGTGCGGAGAATGGCCGACGGATCACCGTGCTGGTTCGATGACCACGGCGCCG
gactgat putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcggaataaatctcttgatgtttagaatgagattcggtcaaaatccgcctcatgcacctaagtctgactaagtggttgactgatcattggtgcgtgtagGAGGAAGGATGGGTGGTCTGCCGGGTGTTCAAGAAGCGGGTGGCGACGGTGCGGAGAATGGCCGACGGATCACCGTGCTGGTTCGATGACCACGGCGCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - gaataaa
- - - - - - - cttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - atgcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgactg