Sequence
atgc intronic sequence ATGC exonic sequence...tagtaacaatactctaaatcccatacgtaaacctaactctattgcaaaagataacttaatttcaactgttctgtggttaaatggcatataactacttcagGTCAGTGGAATGCCTACATTTGCCCTTCCTGTTCAAGATGGTGGGGTTGGTTTTGATTATCGCCTTCATATGGCTGTTCCTGACAAATGGATTGAACTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g32660.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 14
--tagtaacaatactctaaatc--ccatacgtaaacctaactctattgcaaaagataacttaatttcaactgttctgtggttaaatggcatataactacttcagGTCAGTGGAATGCCTACATTTGCCCTTCCTGTTCAAGATGGTGGGGTTGGTTTTGATTATCGCCTTCATATGGCTGTTCCTGACAAATGGATTGAACTCC
| | || | || || ||| | ||| | | | ||| ||| || | | ||| ||| | | ||| |||||||| ||||||| |||||||||||||||||||||||||||||||| ||||||||||| |||||||| ||||| | ||||||||||| |||||||||||||||| || |
ggcaagatcattggcttacataaaccaataggaaatttgaatttatctaaaataatttgtgagttttcttggttat----tcaaaaattatataacttgttcagGTTAGTGGAATGCCTACATTTGCCCTTCCTGTTCACGATGGTGGGGTAGGTTTTGACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTC
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 14
----tagtaacaatactctaaatcccatacgtaaacctaactctattgcaaaagataacttaatttcaactgttctgtggttaaatggcatataactacttcagGTCAGTGGAATGCCTACATTTGCCCTTCCTGTTCAAGATGGTGGGGTTGGTTTTGATTATCGCCTTCATATGGCTGTTCCTGACAAATGGATTGAACTCC
| | || | ||| | ||| | ||| || | | || || || | ||| | || | | | | | | ||||| ||||||||||||||||| ||||||| |||||||||||| |||| |||||||||||||| || ||||| || | ||||| |||||||| | |
taactgttgtaaagagcaaaaagacaatatgatgtttgaaccctctatttgactgtatgaaaactt--gcagttgacaattcaattttctttccatt--tccagGTGAGTGGAATGCCTACATTCTGCCTTCCTACACAAGATGGTGGGATTGGCTTTGATTATCGCCTGCACATGGCCATTGCAGACAAGTGGATTGAGATTC
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 14
--------------------------------------tagtaacaat--actctaa--atcccatacgtaaacctaactctattgcaaaa-gataacttaatt-tcaactgttctgtggttaaa-tggcatataactactt-----------------cagGTCAGTGGAATGCCTACATTTGCCCTTCCTGTTCAAGATGGTGGGGTTGGTTTTGATTATCGCCTTCATATGGCTGTTCCTGACAAATGGATTGAACTCC
| ||||| | | || || | | || | ||| | ||| | ||| | | || || | | |||| ||| ||| | | || | | ||||| ||||||||||| ||||| ||||||| ||||||||||||||||| |||||||||||||| || ||||| || | ||||| |||||||| | |
gtatgttgtcctcttaaagttttgaattaatgtacttctgttaacattttattcaaactgttttaggagttgagtgaacaaaaagacaatatgatgattgaaccctctatttgactgtatgaaaactggtagttgacaattcaattttctttccatttccagGTGAGTGGAATGCCAACATTCTGCCTTCCTACGCAAGATGGTGGGGTTGGCTTTGATTATCGCCTGCACATGGCCATTGCAGACAAGTGGATTGAGATTC
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 14
tagtaacaatactctaaatcccatacgtaaacctaactctattgcaaaagataacttaatttcaactgttctgtggttaaatggca--tataactactt--cagGTCAGTGGAATGCCTACATTTGCCCTTCCTGTTCAAGATGGTGGGGTTGGTTTTGATTATCGCCTTCATATGGCTGTTCCTGACAAATGGATTGAACTCC
|| || | | | | || || | || || | | | ||| || | ||| | || ||| ||| ||| | | || ||||| || |||||||| |||| ||||||||||||||||||| || || |||||||||||| | |||||||| || |||| ||||||||||| || |
taa-aatagtgatttttttctaatgcactaag--aatctgtctatggatgctaatccaagga-attggttttctgtttatgatgcaattatttccattttgcagGTGAGCGGAATGCCAGCATTCTGTATTCCTGTTCAAGATGGTGGTGTGGGATTTGATTATCGCTTACATATGGCCATTGCTGATAAATGGATTGAGCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaagataacttaatttcaactgttctgtggttaaatggcatataactacttcagGTCAGTGGAATGCCTACATTTGCCCTTCCTGTTCAAGATGGTGGGGTTGGTTTTGATTATCGCCTTCATATGGCTGTTCCTGACAAATGGATTGAACTCC
atataac putative branch site (score: 3)
ctacttc CT-rich tract
ataacttaatttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagtaacaatactctaaatcccatacgtaaacctaactctattgcaaaagataacttaatttcaactgttctgtggttaaatggcatataactacttcagGTCAGTGGAATGCCTACATTTGCCCTTCCTGTTCAAGATGGTGGGGTTGGTTTTGATTATCGCCTTCATATGGCTGTTCCTGACAAATGGATTGAACTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT