Sequence
atgc intronic sequence ATGC exonic sequencegtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctctaaccatggcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g50320.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G832989_T01 (Zea mays), 3'ss of exon 6
-gtaacatcctttactgttgctttcggataatc---------ttcactg-ttctgtacgcaaaaaagttgacccatgctaatctctaaccatggcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
| || ||| ||| ||| | | || || | || |||| ||| ||| | | |||| ||||| | ||| |||| |||| |||||| |||| ||||||| ||||||||| ||||| || || |||||||| ||||| || ||||||||||| || ||||| ||||||||||||||||||||||
tagatcaatcttcact--tgcaaacaggccattactctgcaatttattgattctttacacaatcatat-gacctgtgctattttcttttcatgacacaattagGAAGAAAAGAAAATTCGTGACCGTGAACTTGCTCGAGCTAAAGTTACTGCAAATAGGGTTGCTGTTGTGGTCGCAAACGAGTGGAAAGATGCTAATGACA
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 6
-------------gtaacatcctttactgttgctttcggataatct--tcactgttctgtacgcaaa-aaagttgacccatgcta-atctctaaccatggcac-acttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
| || ||||||| || | | | | ||| | || | | ||| | || | || | || || | ||||| |||||||||| ||||||||| ||| | || || || || || |||||||||||||| ||||| || ||||||||||| |||||||||||||||||||
gtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 6
------------------gtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctctaacca---tggcacactt-agGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
| ||| | | ||| || |||||| | | || | ||| | | | | | | || || ||| |||| |||||||||| ||| ||| | ||| | || || || || || |||||||||||||| |||||||| ||||||||||| ||||||||||| ||||| |
gtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagttaagatcatatttatttttgcatggtttatttgacattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 6
-----------------gtaacatc-ctttactgttgctttcggataatctt--cactgttctgtacgcaaaaaagttgacccatgctaatctctaaccatggcac-acttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
||| | || | || | || ||| | ||||| || || | || | ||| || | || ||| | ||||| |||||||||| ||||||||| ||| | || || || || || |||||||||||||| ||||| || ||||||||||| |||||||||||||||||||
gtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcatcttaattgttgc--atgatttgttttgacactatatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 6
------------------gtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctctaacca---tggcacactt-agGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
| ||| | | ||| || |||| | ||| ||| | ||| | | | | | || || ||| ||||||||||||| | ||| ||| | ||| | || || || || || |||||||||||||| |||||||| ||||||||||| ||||||||||||||||| |
gtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaacatcctttactgttgctttcggataatcttcactgt-tctgtacgcaaaaaagttgacccatgctaatctctaaccatggcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
| ||| | | | || | | ||| ||| ||| ||| | | || ||| | | | |||| ||| |||||| ||||||||| || |||||||| ||||| |||||||||||||||||||| || ||||||||||| |||||||||| |||||| |
-----gtaagttaatacatttccgaaaaaagaagtatagaatctttactcaa-----ctgatgaaggaatatttcttgctcta-cttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgc-----taatctctaaccatggcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
||||| ||| || | | ||| | | | ||| | || | || ||| |||| | || | | |||| || | |||| ||||||||| |||||||| || ||||| |||||||||||||||||||| ||| || ||||||||||||||||||| |||||| |
gtaactaaacacact-------tcataaagtctctaatttcttgtcacaacaattgcctactgatgtaggaataattcttgtttttgtct--ttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------------gtaa--catcctttactgttgctttcggataatcttcac-tgttctgtacgcaaaaaagttgacccat-gctaatctctaaccatggcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
| || ||| || | ||| | || || | | | | | | | ||| | | || | | | | || | ||||||||||||||| || ||| | ||||| || || ||||| || || |||||||| || || || || || |||||||| |||||||||||||||||||
gtaatgtgccatttttaaacaataaatattgaacattgcaagtcatttcaggcttatatttttgcatctagttggcatatgccatgtgttctatcattgttgagttgtctttccttttcttttggaccttcagGAGGAAAGAAAAACCCTCGACAGGGAGCTGGCCCGTGCAAAGGTAACTGCAAACAGGGTGGCAGTAGTTGTAGCAAATGAATGGAAAGATGCTAATGACA
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S31_77V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------------gtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctctaacc--atggcacactt-------agGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
| | | | | ||||| || | || || | | | || | | | || ||| || | ||| | ||| | |||| | | || | | || | || | |||||||| ||| ||||||| ||||||||||| ||||| ||||||||||||||||| ||||| |||||||
gtaaaatttatggttttcggggttgaaaatattctccttgtgaatgccgcgagaagttattacgttgcgtt-gaatgatttcttgaagattctttgctatggttattgcttatattaagtcttatctggatgacgcacatttgaaacagGAAGGGAAGAAGACATTGGAGAGGGAATTGGCGCGGGCGAAAATTACAGCTAACAGAGTTGCAGTTGTTGTTGCAAATGAGTGGAAGGATGCAAATGACAMapped 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|25777864|gb|CA752614.1|CA752614EST: CAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAAT GAGGAAAGAAAAATTCTTGACCGTGAGCTTGCTCGGGCAAAAGTTACAGCA
genomic: CAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcct ... gcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCA
EST:
gi|86495989|gb|CI138622.1|CI138622EST: CTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAAT GAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCA
genomic: CTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcct ... gcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttctgtacgcaaaaaagttgacccatgctaatctctaaccatggcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
ctctaac putative branch site (score: 2)
aaaaaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctctaaccatggcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG