Sequence
atgc intronic sequence ATGC exonic sequence...aagatatgatagtatgtgcaacacaattacaaaaattatgcagcattatgcaagtatttgctttccaatcagacaatcttgtcttttgatctgttttcagGCATATGAGAAAGGACTGATGATAGCAGTCATTCCATTCACTTCAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g01240.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G457909_T01 (Zea mays), 3'ss of exon 4
-aagatatgatagtatgtgcaacacaattacaaaaattatgcagcattatgcaagt-atttgctttccaatcagacaatcttgtcttttgatctgttttcagGCATATGAGAAAGGACTGATGATAGCAGTCATTCCATTCACTTCAAAG
| | | ||| | || | | | | || | ||| ||| ||| | | |||||| | | | | |||||||||||||||||||| ||||||| | ||||| |||||||||||||||
ctgtgttttttggtaaaatttatgtgcttcctgaggt-gtacaattcacttcaatcgattcaatttgtctgctcataatctt-tggagaattttttcttcagGCATATGAGAAAGGATTGATGATTGTGGTCATACCATTCACTTCAAAG
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G179406_T01 (Zea mays), 3'ss of exon 6
-aagatatgatagtatgtgcaacacaattacaaaaattatgcagcattatgcaagt-atttgctttccaatcagacaatcttgtcttttgatctgttttcagGCATATGAGAAAGGACTGATGATAGCAGTCATTCCATTCACTTCAAAG
| || | | ||| | || | | | | || | ||| ||| ||| | | |||||| | | | | |||||||||||||||||||| ||||||| || ||||| |||||||||||||||
cagtattttttggtaaaatttatgtgcttcctgaggt-gtacaattcacttcaatcgattcaatttgtctgctcataatctt-tggagaattttttcttcagGCATATGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G481210_T01 (Zea mays), 3'ss of exon 2
-aagatatgatagtatgtgcaacacaattacaaaaattatgcagcattatgcaagt-atttgctttccaatcagacaatcttgtcttttgatctgttttcagGCATATGAGAAAGGACTGATGATAGCAGTCATTCCATTCACTTCAAAG
| | | ||| | || | | | | || | ||| ||| ||| | | |||||| | | | | |||||||||||||||||||| ||||||| || ||||| |||||||||||||||
ctgtgttttttggtaaaatttatgtggttcctgaggt-gtacaattcacttcaatcgattcaatttgtctgctcataatctt-tggagaattttttcttcagGCATATGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G419699_T01 (Zea mays), 3'ss of exon 3
-aagatatgatagtatgtgcaacacaattacaaaaattatgcagcattatgcaagt-atttgctttccaatcagacaatcttgtcttttgatctgttttcagGCATATGAGAAAGGACTGATGATAGCAGTCATTCCATTCACTTCAAAG
| | | ||| | || | | | | || | ||| ||| ||| | | |||||| | | | | |||||||||||||||||||| ||||||| || ||||| |||||||||||||||
ctgtgttttttggtaaaatttatgtgcttcctgaggt-gtacaattcacttcaatcgattcaatttgtctgctcataatctt-tggagaattttttcttcagGCATATGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G414487_T01 (Zea mays), 3'ss of exon 5
-aagatatgatagtatgtgcaacacaattacaaaaattatgcagcattatgcaagt-atttgctttccaatcagacaatcttgtcttttgatctgttttcagGCATATGAGAAAGGACTGATGATAGCAGTCATTCCATTCACTTCAAAG
| | | ||| | || | | | | || | ||| ||| ||| | | |||||| | | | | ||||||||| |||||||||| ||||||| || ||||| |||||||||||||||
ctgtgttttttggtaaaatttatgtgcttcctgaggt-gtacaattcacttcaatcgattcaatttgtctgctcataatctt-tggagaattttttcttcagGCATGTGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G435765_T02 (Zea mays), 3'ss of exon 2
-aagatatgatagtatgtgcaacacaattacaaaaattatgcagcattatgcaagt-atttgctttccaatcagacaatcttgtcttttgatctgttttcagGCATATGAGAAAGGACTGATGATAGCAGTCATTCCATTCACTTCAAAG
|| | | ||| | || | | | | || | ||| ||| ||| | | |||||| | | | | |||||||||||||||||||| ||||||| || ||||| |||||||||||||||
ctgtattttttggtaaaatttatgtgcttcctgaggt-gtacaattcacttcaatcgattcaatttgtctgctcataatctt-tggagaattttttcttcagGCATATGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 19
lower sequence: PP1S85_31V6.1 (Physcomitrella patens), 3'ss of exon 20
-------------------------------------------------------------------------------aagatatgatagtatgtgcaacacaattacaaaaattatgcagcattatgcaagtatttgctttcc-aatcagacaatcttgtcttttgatctgttttcagGCATATGAGAAAGGACTGATGATAGCAGTCATTCCATTCACTTCAAAG
| | || || || | | || | | || || | | | | |||| ||| || || | || || ||| | |||||||||||||||||||||||||| ||| | ||||| ||||| || |||
gttagcatctattcctcacatttgcaatcagaatgtaccataactggcaattcgtctctttattgtgtttcttggttatacttctcgttaagat-tgtgaaccgtatatatatat-atatattttcttttctttttttgttttaagaaatgaactacctgtaaattcgattgtaatgcagGCATATGAGAAAGGACTGATGATTGCAATTATTCCTTTCACATCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgcaagtatttgctttccaatcagacaatcttgtcttttgatctgttttcagGCATATGAGAAAGGACTGATGATAGCAGTCATTCCATTCACTTCAAAG
ttttgat putative branch site (score: 4)
tctgttttc CT-rich tract
aagtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagatatgatagtatgtgcaacacaattacaaaaattatgcagcattatgcaagtatttgctttccaatcagacaatcttgtcttttgatctgttttcagGCATATGAGAAAGGACTGATGATAGCAGTCATTCCATTCACTTCAAAG
- - - - - - tatgtgc
- - - - - - - - - - acacaat
- - - - - - - - - - - - - - acaaaaa
- - - - - - - - - - - - - - - - - -ttatgca
- - - - - - - - - - - - - - - - - - - tgcagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctttc