Sequence
atgc intronic sequence ATGC exonic sequence...cctaataagcataagcaaatgctgcggatatatatcttaattatattagaggatgcatgctagaaattaatctgacccaatgcttctctgatatatgcagCCGTACCACAAAAACATCCAGGTGCCTTAACTTAGGTTCCTACAATTACCTTGGCTTTGCTGCGGCAGATGAATACTGCACTCCTCGTGTTATTGAGTCA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g70370.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g70370.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 3
-cctaataagcata-agcaaatgctgcggatatatatcttaattatattagaggatgcatgctagaaattaatctgacccaatgcttctctgatatatgcagCCGTACCACAAAAACATCCAGGTGCCTTAACTTAGGTTCCTACAATTACCTTGGCTTTGCTGCGGCAGATGAATACTGCACTCCTCGTGTTATTGAGTCA
| || | || | || || | || || | ||| | | || | || ||| | |||| ||| ||| ||| |||| |||| ||||||||| |||| ||| ||||||||||| |||||||| || |||||||| ||||||||||| ||||| |||||||| ||||||||||||||||||
gtgtgttactcttacattgcatcctatagtaatttagc--aatcgtctcagcg--tggatgtcaa-----catctaacctggtgcatctttgat----gcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCTTGGTTTTGCTGCGGCTGATGAGTACTGCACCCCTCGTGTTATTGAGTCA
upper sequence: LOC_Os01g70370.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 3
cctaataagcataagcaaatgctgcggatatatatcttaa-ttatattagaggatgcatgctagaaattaatctgacccaatgcttctctgatatatgcagCCGTACCACAAAAACATCCAGGTGCCTTAACTTAGGTTCCTACAATTACCTTGGCTTTGCTGCGGCAGATGAATACTGCACTCCTCGTGTTATTGAGTCA
| | | ||| | || || || | || | | | | | || || || || | | | | ||||| |||||| || || |||| | || |||||||| || || || ||||| || ||||| ||||| || ||||||||||||||||| ||||| || |||| |
-ttgaaatatatatatatttgttgtaaattttaatttagagcttcagcatgagaaatatatctgatgcctatttttcatactatttctcctcccaatgcagACGGACTGATAAAATAAGTAGATGCCTTAATTTGGGATCATACAACTATCTTGGTTTTGCGGCAGCAGATGAATACTGCACGCCTCGAGTAGTTGATACG
upper sequence: LOC_Os01g70370.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------cctaataagcataagcaaatgctgcggatatatatcttaattatattagaggatgcatgc---tagaaattaatctgaccc--------------aatgcttctctgata-------tatgcagCCGTACCACAAAAACATCCAGGTGCCTTAACTTAGGTTCCTACAATTACCTTGGCTTTGCTGCGGCAGATGAATACTGCACTCCTCGTGTTATTGAGTCA
|||| | || || | | |||| | | ||| | |||| ||| | | |||| | | | | ||| || || | | ||||| || || ||||| || |||||||||||| || |||||||||||||| ||||| |||| | | |||||||| ||||| |||||||| ||||||||
gtgagtctgtcttcctctgcttttttttctgttgaacaattataatttctttggtcacattaagagaatatgaaaccaaatgtaaaggttggattcatacggttgagaattggtttatcacttaggatgtcaaagaataaacctttggttgcaactctgtgcagGCGAACTACAAAGACTAGCAGGTGCCTTAATTTGGGTTCCTACAATTATCTTGGATTTGGTTCTTTCGATGAATATTGCACGCCTCGTGTCATTGAGTCT
upper sequence: LOC_Os01g70370.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 3
cctaataagca-taagcaaatgctgcggatatatatcttaattatattagaggatgcatgctagaaattaatctgacccaatgcttctctgatat-atgcagCCGTACCACAAAAACATCCAGGTGCCTTAACTTAGGTTCCTACAATTACCTTGGCTTTGCTGCGGCAGATGAATACTGCACTCCTCGTGTTATTGAGTCA
| | || | | | | ||| || || || | | | | | | | | ||||| | | | | | ||| | |||||| || || | || | | ||||||||||| || || ||||| ||||||||||||||||| | |||||||||||||| || ||||| ||||| |||
tatggtgcacaatgatttatggttgccctgatttacatt--ctccagtgtaagctaaaactcataaatttttagtatctatcaactaatcgatttcatgcagACGAACTAGCAATATCAGTCGATGCCTTAACTTGGGATCATACAACTACCTTGGCTTTGCTGCATCGGATGAATACTGCACGCCACGTGTAATTGAATCA
upper sequence: LOC_Os01g70370.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 3
cctaataagcataagcaaatgctgcggatatatatcttaattatattagaggatgcatgctagaaattaatctgacccaatgcttc--tctgatat-atgcagCCGTACCACAAAAACATCCAGGTGCCTTAACTTAGGTTCCTACAATTACCTTGGCTTTGCTGCGGCAGATGAATACTGCACTCCTCGTGTTATTGAGTCA
|||||| | | | ||| | | | | || || | || | | ||| || | | || || | || | |||||| || |||||||| | | | ||| |||||||| || || |||||||||||||| ||||| || ||||||||| |||||| || ||||| || |||||
-ttaataaagtttttgtatggttgcttgttgggagtctcttggattttgactcaacctg--aaatatttggtggatcaattgatttggttcaatctcatgcagACGAACCACAAAGATAAGTAAGTGTCTTAACTTGGGGTCATACAATTACCTTGGATTTGCCGCATCAGATGAATTCTGCACACCACGTGTAATCGAGTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagaggatgcatgctagaaattaatctgacccaatgcttctctgatatatgcagCCGTACCACAAAAACATCCAGGTGCCTTAACTTAGGTTCCTACAATTACCTTGGCTTTGCTGCGGCAGATGAATACTGCACTCCTCGTGTTATTGAGTCA
tagaaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctaataagcataagcaaatgctgcggatatatatcttaattatattagaggatgcatgctagaaattaatctgacccaatgcttctctgatatatgcagCCGTACCACAAAAACATCCAGGTGCCTTAACTTAGGTTCCTACAATTACCTTGGCTTTGCTGCGGCAGATGAATACTGCACTCCTCGTGTTATTGAGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - -agcataa
- - - - - - - - - -tgctgcg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgc