Sequence
atgc intronic sequence ATGC exonic sequence...tagtagtagttttttttgttaatgggagtagaagaatcaaatgaccaatatttgttcagagattttaattagggcataaaaaatccttggttatgtatagGCATCGGTGGACCGGAAGGTACGAGGCGCATCTGTGGGATAACAGCTGCCGGCGTGAGGGCCAGAGCCGCAAGGGACGCCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g55970.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g55970.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G086573_T01 (Zea mays), 3'ss of exon 2
tagtagtagttttttttgttaatgggagtagaagaatcaaatgaccaatatttgttcagagattttaa----ttagggcataaaaaatccttggttatgtatagGCATCGGTGGACCGGAAGGTACGAGGCGCATCTGTGGGATAACAGCTGCCGGCGTGAGGGCCAGAGCCGCAAGGGACGCCAAG
|| | | | || | | || | | | || ||| | | ||| ||||| || || ||||| || | |||||| |||||||| || ||||||||||| ||||||||||| ||||||||||| || || || |||||||||||||| |||||||
----agaaaaaaataacaagcagtcaagctgcaccatatattattaattacgggttttgtctgtctaaaatcttaggtgatgtggtatttttggtgatttctagGCACCGGTGGACTGGCAGGTACGAGGCACATCTGTGGGACAACAGCTGCCGACGCGAAGGGCAGAGCCGCAAGGGCCGCCAAG
upper sequence: LOC_Os04g55970.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 2
-----tagtagtagttttttttgttaatgggagtagaagaatcaaatgacca-atatttgttcagagattttaattagggcataaaaaatccttggttatgtatagGCATCGGTGGACCGGAAGGTACGAGGCGCATCTGTGGGATAACAGCTGCCGGCGTGAGGGCCAGAGCCGCAAGGGACGCCAAG
||| || | ||| || | || |||| | | || | | || ||| || ||| || | ||| || | ||||||||| ||||| ||| |||||||||| ||||||||||| || | || | || || || | ||||| || || ||||
gggtgtag-agctgaatttaggcttggcgaaggtcgaagtggttgagggtcatgtcctggtctgaggatgttgg--ggggtgtattgtgtgtttgatt---tgtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
upper sequence: LOC_Os04g55970.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
-----tagtagtagttttttttgttaatgggagtagaagaatcaaatgaccaatatttgttcagagattttaattagggcataaaaaatccttggttatgtatagGCATCGGTGGACCGGAAGGTACGAGGCGCATCTGTGGGATAACAGCTGCCGGCGTGAGGGCCAGAGCCGCAAGGGACGCCAAG
|| |||| | | || |||| | | || || || ||| | || ||| | | | || | || | ||||||||| ||||| ||| |||||||||| ||||||||||| || | || | || || || | ||||| || || ||||
ggcgcagagagctaaattttagcctggcgaaggtcgaagttgttgagggtcatatcctggtctgaggat---gttggggggtgtattgtg--tgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatatttgttcagagattttaattagggcataaaaaatccttggttatgtatagGCATCGGTGGACCGGAAGGTACGAGGCGCATCTGTGGGATAACAGCTGCCGGCGTGAGGGCCAGAGCCGCAAGGGACGCCAAG
ttttaat putative branch site (score: 3)
agagattttaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagtagtagttttttttgttaatgggagtagaagaatcaaatgaccaatatttgttcagagattttaattagggcataaaaaatccttggttatgtatagGCATCGGTGGACCGGAAGGTACGAGGCGCATCTGTGGGATAACAGCTGCCGGCGTGAGGGCCAGAGCCGCAAGGGACGCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC