Sequence
atgc intronic sequence ATGC exonic sequence...tattaagtactttcttaatatttatgtctttttatttgattttaaatttgatttgattcttgtgttgtgcattggcgcgcatgcattgatgcatatgcagGTGTTTGATTTCGCGGACAAATACAGGGGATCATACAGCGACTCGCTGAGCTCAGTGGTGTGTCCGTTCTACTGCTCCCACTCCTACCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g03120.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g03120.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G141911_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------tattaagtactttcttaatatttatgtctttttatt-tgattttaaatttgatttgattcttgtgttgtgcattggcg---cgcatgcattgatgcatatgcagGTGTTTGATTTCGCGGACAAATACAGGGGATCATACAGCGACTCGCTGAGCTCAGTGGTGTGTCCGTTCTACTGCTCCCACTCCTACCAT---
| || | | | | | | ||| | | || |||| || | | | | || ||| | ||| ||||||||||||| ||||||||| |||||||| || |||||||||||||| ||||| |||| || ||||||||||||||| |||| | |
gtacgcgtgcagtcacatctcacatgacatgcctctgccttgctcttgggcggcgtgcgtgcgtgcccgcccgtgagccgtgacgcgacgtgtgccctgatcctctgatccgtcgtcgtcgtgtcgcgctcgcgcgtgcgcttgcagGTGTTTGACTTCGCGGACCGGTACAGGGGCTCGTACAGCGACTCGCTCAGCTCCGTGGCCTGCCCGTTCTACTGCTCCTACTCTGGCTACCAG
upper sequence: LOC_Os02g03120.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0025g02650.t01 (Vitis vinifera), 3'ss of exon 3
tattaagtactttcttaatatttatgtcttttta-tttgattttaaatttgatttgattcttgtgttgtgcattggcgcgcatgcattgatgcatatgcagGTGTTTGATTTCGCGGACAAATACAGGGGATCATACAGCGACTCGCTGAGCTCAGTGGTGTGTCCGTTCTACTGCTCCCACTCCTACCAT---
||| ||| | | ||| || || ||| | ||| | || | || | | | ||| ||| | || | || | ||| ||||||||||||||||||| || | ||||| || || ||||||||||| || ||||| ||||| || || |||||||||||| |||| ||
--gtaaacactccc---acattaatctcctttcaatttcttcctatgtctg---taaattttg-attgaaaactgagttgattgtaatga------tgcagGTGTTTGATTTCGCAGATAGCTACAGAGGGTCTTACAGCGACTCTCTCAGCTCGGTGGTCTGCCCATTCTACTGCTCCTACTCTGGATATCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgatttgattcttgtgttgtgcattggcgcgcatgcattgatgcatatgcagGTGTTTGATTTCGCGGACAAATACAGGGGATCATACAGCGACTCGCTGAGCTCAGTGGTGTGTCCGTTCTACTGCTCCCACTCCTACCAT
cattgat putative branch site (score: 4)
atttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattaagtactttcttaatatttatgtctttttatttgattttaaatttgatttgattcttgtgttgtgcattggcgcgcatgcattgatgcatatgcagGTGTTTGATTTCGCGGACAAATACAGGGGATCATACAGCGACTCGCTGAGCTCAGTGGTGTGTCCGTTCTACTGCTCCCACTCCTACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcatgc