Sequence
atgc intronic sequence ATGC exonic sequencegtactggcctcttcattgtccgataaaatgcttatgctcacttgtacggtgcacagtttgctaatggaaacttatgttctttcagTCGAGAGCAACTGGAGTGGTGGTTGATTTCAGTGAACCTTCAACTGTTTATGACAATGTCAAACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g02570.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g02570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G044247_T01 (Zea mays), 3'ss of exon 3
------------------------------gtactggcctcttcattgtccgataaaatgcttatgctc--acttgta-cggtgcacagtttgctaatgg---aaacttatgttc--tttcagTCGAGAGCAACTGGAGTGGTGGTTGATTTCAGTGAACCTTCAACTGTTTATGACAATGTCAAACAG
| | | | | | | ||| | | ||||| | | || | ||| | | ||| ||| || |||||||||||||| || |||||||| || ||||| || |||||| ||||||| ||||||||||| |||
gtacagaccccgctcagctcgctgggggccgggcgaccgtgataaatccccggcgggcttcgggcttcaggacttgcatctttgggctaactgcacactgcctgtccttccattccattccagTCGAGAGCAACCGGCGTGGTGGTCGACTTCAGCGAGCCTTCAGCTGTTTACGACAATGTCAAGCAG
upper sequence: LOC_Os03g02570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv16s0100g00480.t01 (Vitis vinifera), 3'ss of exon 3
--------gtactggcctcttcattgtccg-ataaaatgctt------atgctcacttgtacggtgcacagtttgctaatggaaacttat----gttctttcagTCGAGAGCAACTGGAGTGGTGGTTGATTTCAGTGAACCTTCAACTGTTTATGACAATGTCAAACAG
||| ||| || ||||| | |||| ||| | || || ||| | || | || || ||| | || | | || ||||| | ||| ||||| |||||||||||||||| ||| ||||| || |||||||| ||||| ||||||
gatagaaagtaatggaatcaa-attgtacatataacatgttgtgattgattctaccttatcgtgtttatgcttcactgatgaactgtttttggaatgctagCAGTCAAAAGCCACTGGGGTGGTGGTTGATTTCACTGATCCTTCTACAGTTTATGAAAATGTGAAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttatgctcacttgtacggtgcacagtttgctaatggaaacttatgttctttcagTCGAGAGCAACTGGAGTGGTGGTTGATTTCAGTGAACCTTCAACTGTTTATGACAATGTCAAACAG
tgctaat putative branch site (score: 2)
tgttctttc putative PPT
aaacttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactggcctcttcattgtccgataaaatgcttatgctcacttgtacggtgcacagtttgctaatggaaacttatgttctttcagTCGAGAGCAACTGGAGTGGTGGTTGATTTCAGTGAACCTTCAACTGTTTATGACAATGTCAAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG