Sequence
atgc intronic sequence ATGC exonic sequencegtacgtacattgtcctctcgttccgatcgatgcgtacgtgtctttctttaatttacttatggcgttgcgcgcgtacgtgcagTGGGGTGGGGGTGCTATGGCGCGGCGGCGGCGCAGTACGGGAGGAGGGTGGAGGACCCGGAGCCGGGGCGGTGCCGGCGTACGGACGGCAAGAAGTGGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g10310.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g10310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G850129_T01 (Zea mays), 3'ss of exon 1
------------------------------------------gtacgtacattgtcctctcgttccgatc---gatgcgtacgtgtctttctttaatttacttatggcgttgcgcg------cgtacgtgcagTGGGGT---GGGGGTGCTATGGCGCGGCGGCGGCGCAGTACGGGAGGAGGGTGGAGGACCCGGAGCCGGGGCGGTGCCGGCGTACGGACGGCAAGAAGTGGCG
|| | | | | | || || |||| || | | | || | || ||| | ||| || ||| | |||||||| || |||| ||||| ||||||| |||| || | | | | || ||||||| |||||||||||||||||||||| |||||||||||||||||
gtacgacctgcgcgcttctctcctcccgacccgacctcccccgtcctcgcctcatgtt-tcactctgatcatcgacagccatcagcccatcacatcatcgctgatgactttgtacgtgtgaccgtgcatgcagTGGCGTACTGGGGCTGCTACGGCGCGGGGGCGCCGTTCGGCCGCAAGGCGGCGGAGGACACGGAGCCGGGGCGGTGCCGGCGGACGGACGGCAAGAAGTG---
upper sequence: LOC_Os06g10310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G067743_T03 (Zea mays), 3'ss of exon 1
------------gtacgtacattgtcctctcgttccgatcga-----tgcgtacgtgtctttctttaat-------------------ttacttatggcgttgcgcg-----cgtacgtgcagTGGGGTGGGGGTGCTATGGCGCGGCGGCGGCGCAGTACGGGAGGAGGGTGGAGGACCCGGAGCCGGGGCGGTGCCGGCGTACGGACGGCAAGAAGTGGCG
| | | | ||| | | | ||||| ||| ||||| || | | || | || | | || || || || ||||||| || || ||| | |||| ||||| || ||| | | || ||||||||||||||| |||||||||||||| ||||||||||||||||||||
gtacgcccccgcgcgcttctctcctcccccctccctcatcgagttcccgcgctcgtgttttacactcatcgtcgatagatagtcgtcgtcgctgacgagtctgtacgtgccccgcgcgcgcagTGGCGTACTGGGGCTGCTATGGCGCGGGGGCGCCGTTCGGCCGCAAGGCGGAGGACCCGGAGCCCGGGCGGTGCCGGCGGACGGACGGCAAGAAGTGGCG
upper sequence: LOC_Os06g10310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ24024 (Selaginella moellendorffii), 3'ss of exon 2
----gtacgtacattgtcctctcgttccgatcgatgcgtacgtgtctttctttaattt---acttatggcgttgcgcgcgtacgtgcag-
|| | | | | | ||| || ||| || || || | | || | || | || | | | |||| ||| || | | ||| | | ||||||||||| || |||||||| || || ||||||||||||||| |
gtgagtgcctgctgcctttctcccttcacttcactgctcgactgcctcctcgctgttctcagcaccttgcaccactggcaactctaaagatctccttgctttcctgtgcagTGGGCTGGGGAAACTTCCACCTTGGAATTCCGAACAATCCCGACCCGGAGCCTGGTCGGTGCCGACGAACAGACGGCAAGAAGTGGAGGTGCTCCAGGGA
upper sequence: LOC_Os06g10310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ24588 (Selaginella moellendorffii), 3'ss of exon 2
--------gtacgtacattgtcctctcgttcc---gatcga-tgcgtacgtgtctttct-------ttaatttacttatggcgttgcgcgcgtacgtgcagTGGGGTGGGGGTGCTATGGCGCGGCGGCGGCGCAGTACGGGAGGAGGGTGGAGGACCCGGAGCCGGGGCGGTGCCGGCGTACGGACGGCAAGAAGTGGCG------------
| | | || ||| || | | | |||| ||| | | | | |||| || ||| | | | | ||| | ||| | || ||| | | | | | | | | | |||||||||| || |||||||| || || ||||||||||||||| |
gtgagtgcctgctgcctttctcccttcacttcactgctcgactgcctcctcgccgttctcagcaccttgcaccactggcaactctaaagatctccttgctttcctgtgcag- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgatgcgtacgtgtctttctttaatttacttatggcgttgcgcgcgtacgtgcagTGGGGTGGGGGTGCTATGGCGCGGCGGCGGCGCAGTACGGGAGGAGGGTGGAGGACCCGGAGCCGGGGCGGTGCCGGCGTACGGACGGCAAGAAGTGGCG
ctttaat putative branch site (score: 4)
tttctttaatttactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtacattgtcctctcgttccgatcgatgcgtacgtgtctttctttaatttacttatggcgttgcgcgcgtacgtgcagTGGGGTGGGGGTGCTATGGCGCGGCGGCGGCGCAGTACGGGAGGAGGGTGGAGGACCCGGAGCCGGGGCGGTGCCGGCGTACGGACGGCAAGAAGTGGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT