Sequence
atgc intronic sequence ATGC exonic sequencegtacgtacctgcagctactaaagccactgaagtctgaatgtactcattagtatctgttttagcgtctgttttatgtgtacaatgtgtgagtgcagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g14080.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 3
gtacgtacctgcagctactaaagccactgaagtctgaatgtactcattagtatctgttttagcgtctgttttat--gtgtaca-atgtgtgagtg--cagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC
||| | || | || | | ||| | | | | | || || | | ||||| || | | ||||||||||||||||||||||||||||||||||||| |||||||||| |||||||||||||| |||||||| ||||||||||||||||||||||||||||||
-----------------gtaaggttgct--tgcttgctcgctcgcatggttcgccggctaactgtgtgccgcgtaagcgtacatatatactaccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACGACGGTGTTCATCCCGTCGTTCCACAAC
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 3
------------gtacgt-acctgcagctactaaagccactgaagt--ctgaatgtactcattagtatctgttttagcgtctgttttatgtgtacaatgtgtgagtgcagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC
|| | || |||| | | | | || | ||||| | ||||| | | || || || |||| | | ||||| || ||||||||| || ||||| || ||||| |||||||||||||| ||||| ||||||||||| || ||||| || || || || || || || || || ||||||
aagacaaggaaccaacatcacatgcatgtcccataataaccttacctgctgaaacaattcattggggtgtg----agtgtgaattttgt---tttaatgtt---gttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTCGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 4
gtacgtacctgcagctactaaagccactgaagtctgaatgtactcattagtatctgttttagcgtctgttttatgtgtacaatg-tgtgagtgcagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC
||| | | || ||| | ||| ||| || ||||| | ||||| | | | ||| ||||| |||||||| |||||||| ||||||||||| || ||||| |||||||| || || ||||| || || ||||| |||||||| || |||||||||
-----------------gtaagacagtagtagatc--atgattttcttaatattgcattataaactaagtttatatatacaacaatattgtttcagTAACATATACTACATAAACGACAATCTGGACAAGAGAACTTGGACTTACATCTTTGGGGCATGCTGTGCAACAACGGTCTTCATCCCTTCTTTCCACAAC
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 3
-------gtacgtacctgcagctactaaagccactgaagtctgaatgtactcattagtatctgttttagcgtctgttttatgtgtacaatgtgtgagtgcagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC
| | | | || | | ||| | ||| | || | || || | || || | | | | || ||||||||| || ||||| || ||||| |||||||||||||| ||||| |||||||| || || ||||| || || || || || || || || || ||||||
aagacaagaaaccaacatcacatgcatgtcccataataatcttacctcctgcaaca--attcattggggtgtgagtgtgaatattgttttaatgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTTGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 3
------------------------gtacgtacctgcagctactaaagccactgaagtctgaatgtactcatta-gtatctgttttagc--gtctgttttatgtgtacaatgtgtgagtgcagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC
| | | | || | | | | | ||| | |||| | | | | | | | | | || || |||||||||||||||||||| || ||||| | |||||||| || ||||| |||||||||||||| ||||| || ||||| || ||||| || || ||||| ||
gtaaacccaaaaggggaaaggaaaaatcattacaatgtacattatatttctgtttggacagacgaatacatcatgtatacatactggttaatttttcctcaatttccattgatatgctgcagCAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACATCTTCGGCGCCTGCTGTGCTACGACCGTTTTCATTCCTTCATTCCATAAT
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------------------gtacgtacct-gcagctactaaagccactgaagtctgaatgtactcatt-------agtatctgttttag-cgtctgttttatgtgtacaatgtgtgagt-gcagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC
| || || | | || | |||| | | | | | || | | | | || | | | | | || || || || |||||||||| || ||||| || || || |||||||||||||| ||||| ||||||||||| || ||||| || || || || || || || || |||||||||
gcatctccctctctccctccctatcctcctcctactactactctctctctctctctctctctttctctgtctcttgttttttcttcacccaccacatttttttttcctttctttacaataaacaaagatctgaggcattttctgcaactgggcatgtcgtttgttgcagCAACATATATTACATAAATGATAATCTGGACAAGAGGACATGGACTTACATCTTCGGAGCCTGCTGTGCCACCACAGTCTTTATTCCTTCATTCCACAACMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|58652592|gb|CK041272.1|CK041272EST: TGCACCTTCCTACTCTTCGGCTCCGTCATCCAGCTCATCGCCTGCGCTAG CAACATCTACTACATCAACGACAAGCTG
genomic: TGCACCTTCCTACTCTTCGGCTCCGTCATCCAGCTCATCGCCTGCGCTAGgtacgtacct ... gtgagtgcagCAACATCTACTACATCAACGACAAGCTG
EST:
gi|58680652|gb|CK069339.1|CK069339EST: TGCACCTTCCTACTCTTCGGCTCCGTCATCCAGCTCATCGCCTGCGCTAG CAACATCTACTAC
genomic: TGCACCTTCCTACTCTTCGGCTCCGTCATCCAGCTCATCGCCTGCGCTAGgtacgtacct ... gtgagtgcagCAACATCTACTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactcattagtatctgttttagcgtctgttttatgtgtacaatgtgtgagtgcagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC
attagtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtacctgcagctactaaagccactgaagtctgaatgtactcattagtatctgttttagcgtctgttttatgtgtacaatgtgtgagtgcagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC