Sequence
atgc intronic sequence ATGC exonic sequencegtatatgcatatttcagtggcatctttttttacttcctttttggtttcttgatgtgtctaaatgggataagttgctaacagGTATGAGTGATCTACTTTCACCTTTTGTTGTTCTCTATGAGGATGATGCAGATGCCTTTTGGTGCTTTGAGATGCTACTGAGAAGGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g01010.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G031043_T01 (Zea mays), 3'ss of exon 7
gtatatgcatatttc-agtggcatctttttttacttcctttttggt-ttcttgatgtgtctaaatgggataagttgctaacagGTATGAGTGATCTACTTTCACCTTTTGTTGTTCTCTATGAGGATGATGCAGATGCCTTTTGGTGCTTTGAGATGCTACTGAGAAGGATG
| |||||||||| || || | |||| |||| ||| | |||||||||| |||||| ||||| || ||||||||||||||| || |||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
--gtttgcatatttcgaggagccttattttgtactattatttgattattcttgatgtatctaaa-attctaagtaatta-tagGTATGAGTGATCTGCTGTCACCTTTTGTTGTCATATATGAGGATGATGCAGATGCCTTTTGGTGCTTTGAGATGCTACTGAGAAGGATG
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G42150.1 (Glycine max), 3'ss of exon 5
-----------------------------------gtatatgcatatttcagtggcatctttttttacttcctttttggtttcttga---tgtgtctaaatgggataagttgctaacagGTATGAGTGATCTACTTTCACCTTTTGTTGTTCTCTATGAGGATGATGCAGATGCCTTTTGGTGCTTTGAGATGCTACTGAGAAGGATG
|| | || | | | | | |||| | ||| | | | ||| | | | | | | ||| | ||||||||||||| | || || || |||||||| ||| ||||||| |||||||||| |||||||| ||||||||||| | || || |||
gttatttttttcctgggaatttcttgacttcttgctgatgattgtgttctatttatag-tcctattacactgactctggatgccaaaacttgtcttttcactgaaatacttgtttttagGTATGAGTGATTTGCTGTCTCCCTTTGTTGTAATCTTTGAGGATAATGCAGATGCATTTTGGTGTTTTGAGATGCTTTTAAGGAGAATG
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G03240.1 (Glycine max), 3'ss of exon 5
------------------------------------gtatatgcatatttcagtggcatctttttttacttcctttttggtttcttga---tgtgtctaaatgggataagttgctaacagGTATGAGTGATCTACTTTCACCTTTTGTTGTTCTCTATGAGGATGATGCAGATGCCTTTTGGTGCTTTGAGATGCTACTGAGAAGGATG
||| | || | | | | || | |||| | ||| | | | | | | | | | | | ||| | ||||||||| ||| | || || || |||||||| ||| ||||||| |||||||||| |||||||| ||||||||||| | || || |||
gttatattttttcctgggaatttcttgacttcttgctgataattgtgttctatttgtag-ttctattacgctgactctggatgccaaaacttatcttttcactgaaatatttgattttagGTATGAGCGATTTGCTGTCTCCCTTTGTTGTAATCTTTGAGGATAATGCAGATGCATTTTGGTGTTTTGAGATGCTTTTAAGGAGAATG
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0226g00020.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------gtatatgcatatttcagtggcatctttttttacttcctttttggtttcttgatgtgtctaaatgggat----aagttgctaacagGTATGAGTGATCTACTTTCACCTTTTGTTGTTCTCTATGAGGATGATGCAGATGCCTTTTGGTGCTTTGAGATGCTACTGAGAAGGATG
| | | |||| | ||| | | || |||| | | | || | || || | || ||||||||| || | || || |||||||| ||||| | |||||| |||| ||||| |||||||||||||||||||| |||||||| |||
gttgttcctttgtctttttggttgaaccttttccagttgtacaatgattattttcttcatggaaatccatagctggttaattttgtaatatcagctacaattacttataatttggaatcttctcttagGTATGAGCGACTTGCTGTCTCCTTTTGTCGTTCTATTTGAGGACAATGCTGATGCATTTTGGTGCTTTGAGATGCTTCTGAGAAGAATG
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0226g00160.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------gtatatgcatatttcagtggcatct--ttttttacttcctttttggtttcttgatgtgtctaaatgggataag--ttgctaacagGTATGAGTGATCTACTTTCACCTTTTGTTGTTCTCTATGAGGATGATGCAGATGCCTTTTGGTGCTTTGAGATGCTACTGAGAAGGATG
| ||| | | || || | |||| || | | || | ||| | || | | |||| |||||||||||| | || || |||||||| |||||| ||||||| |||| ||||| |||||||||||||||||||| || ||||| |||
gtggtgcctttatctttctgtttgaacctcttccagttgtatgataactattttattcatggaaagctctagataatttggttttgtaatatcagcttaaacacc-aatggttacttgtgacttgaaatctgctcttagGTATGAGTGACTTGCTGTCTCCTTTTGTCATTCTCTTTGAGGATAATGCTGATGCATTTTGGTGCTTTGAGATGCTTCTAAGAAGAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttacttcctttttggtttcttgatgtgtctaaatgggataagttgctaacagGTATGAGTGATCTACTTTCACCTTTTGTTGTTCTCTATGAGGATGATGCAGATGCCTTTTGGTGCTTTGAGATGCTACTGAGAAGGATG
gtctaaa putative branch site (score: 3)
tctaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatgcatatttcagtggcatctttttttacttcctttttggtttcttgatgtgtctaaatgggataagttgctaacagGTATGAGTGATCTACTTTCACCTTTTGTTGTTCTCTATGAGGATGATGCAGATGCCTTTTGGTGCTTTGAGATGCTACTGAGAAGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG