Sequence
atgc intronic sequence ATGC exonic sequencegtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataacgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g41470.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 8
gtatgtaatcataatctctct-gtttatgctcttcatagcacttgcagtctcatatggcttgtatg-tacttgttctat-ataacgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG
||| ||| | ||| | | || | ||| || | || || || |||| ||| || |||| |||| ||| |||||| ||||||||||||||||| ||||||||||| ||||||||||||||||||| |||||||| |||||| |||||||||| ||||||| |
----gtaggcattctttcttttatacattttattcttattagttttag---caaatggaaaacatgatagttgtactatcatactacagGCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGTG
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 8
gtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataac-gcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG
||| | | || || | | | ||| | |||| ||| |||||| || | | | || |||| | || |||||| ||||||||||||||||| ||||||||||| ||||||||||||||||||| |||||||| |||||| |||||||||| |||||||||
gtaagcattcttactttatgcattt-tattcttattagtgcttgcaa----atgaaacaaattgatggctgcgctatcttactacagGCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCG
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------gtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataa-cgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG
| || || ||||| ||| || | | | || || | || | || || || |||| | | ||| | ||||| || ||||| | ||| | |||||||| || ||| ||||| |||||||| |||||||||||||| ||||||| ||| || ||
tgtatcttgtaatctgatcgtcatatgaatctggttgtgtaagattcttg-gttgctcacaatgaaatctca-ttataaatagttgtgttgtttaaatgtagGCTTTGCCTTGGGGCGTGGACAGAGCATGGTGAGAAGACAGGTGGCTTTTATGCTTGTAACCGTTATGAAGCAGCAAAGCAAGATGGCATT
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 8
---------gtatgtaatcataatc--tctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataa---cgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG
| | ||| |||| | | | | || ||| | | || | | | | |||||| ||| || || ||||||| ||||||||| ||||||| || ||||| || |||| ||||| |||||||| ||||||||||||||| |||||| ||| || |||| |
gttatttttttttcaaattttaattcatatttagctttggagttctaaaaatgaacactttgtttcttcatgtatgctcttcgataatgtatgcttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTG
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S178_72V6.3 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------------------------------------------------gtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataacgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG
| | ||| | ||| | | ||| ||||| | | || ||||| || | || || | || | | |||||||||||||||| ||||| | || || || ||||| ||||| || || ||||| |||||||||||||| | || | ||| ||||| | |
gtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcct-cattctcaagtgtagcttttgaaccttgact-tctttggcagGCTGTGTCTTGGAGCATGGACTGATCACGGTGAACGAACTGGAGGTTTCTATGCATGTAACCGTTATGAAACTGCCAAGCAAGAAGGCGTGMapped 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|29681156|gb|CB677431.1|CB677431EST: GGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTG GCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTA
genomic: GGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatc ... tataacgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataacgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG
atataac putative branch site (score: 3)
ttctatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataacgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG