Sequence
atgc intronic sequence ATGC exonic sequence...atttgacaaaatacaaatttagaacctatcatgatctttctcgttaatctatacaaaagatcaactgatcaatacttgcaactgtttcccacaacgacagGGCCTTTGGCTTTGGACGGACAAGAGCTGACATGGAACCATCCTCACAGCCTCAGCCTGTGATGGGTGTTGCCACTGGTGGGTCACAAGCATATCCTCCT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g07450.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g07450.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G311316_T02 (Zea mays), 3'ss of exon 1
------atttgacaaaatacaaatttagaacctatcat-----gatctttctcgttaatctatacaaaagatcaactgatcaatacttgcaactgtttcccacaacgacagGGCCTTT---GGCTTTGGACGGACAAGAGCTGACATGGAACCATCCTCACAGCCTCAGCCTGTGATGGGTGTTGCCACTGGTGGGTCACAAGCATATCCTCCT---
||| || | ||| ||||| | || ||||||| ||| |||| | || || ||||||| | || ||| ||||| ||| | | |||| | || | |||| || |||| || |||||||||||||||||||||||| || |||||||||||| |||||||| | |||||| ||
atacatcttttgcatttttatgtgttataacctgtaattttgtagtctttcttgtttatctggatggaaa---aaatgatcaa-atttccaattgttttcca-agGGTCAGGACACTTATTGATTTTGAACA---AAGATCTAGCATGGAACCATCCTCACAGCCTCAACCAATGATGGGTGTTG---------GGTCACAACCTTATCCTGCTGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatctatacaaaagatcaactgatcaatacttgcaactgtttcccacaacgacagGGCCTTTGGCTTTGGACGGACAAGAGCTGACATGGAACCATCCTCACAGCCTCAGCCTGTGATGGGTGTTGCCACTGGTGGGTCACAAGCATATCCTCCT
aactgat putative branch site (score: 3)
tttcccac putative PPT
atacaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgacaaaatacaaatttagaacctatcatgatctttctcgttaatctatacaaaagatcaactgatcaatacttgcaactgtttcccacaacgacagGGCCTTTGGCTTTGGACGGACAAGAGCTGACATGGAACCATCCTCACAGCCTCAGCCTGTGATGGGTGTTGCCACTGGTGGGTCACAAGCATATCCTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG