Sequence
atgc intronic sequence ATGC exonic sequence...gaaaccaaacaacattttctgttcttcatgtattcttatgtatttttcttgtatctggatacaaaaataaactttttgttatatttctgattaaatgtagGTTGGTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g48300.3 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 5
gaaaccaaacaacattttctgttcttcatgtattcttatg---tatttttcttgtatctggatacaaaaataaactttttgttatat-ttctg---attaaatg----tagGTTGGTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATG
|||| ||| | | | | |||||| ||| || || || ||| | || ||| | ||| ||| | || || |||| || |||||||| || | || ||||||||||| || || || || |||||||||||||||||||| || ||||| ||||| || ||||||||||| ||||| ||||
-----------taatttctggttttcctttcactcttattagttatattactgatagtctgatgtataactaatcaacttgatatctgttttgggtattacattatcttagGTTGGCAATAGGTCCAGTGAATTTCACCCAGAAGTGAGAAGAGTGAGGCGTGAAGGATCCTATATTTATGAGGAATTTATGCCTACTGGAGGGACAGATG
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 7
gaaaccaaacaacattttctgttcttcatgtattcttatgtatttttcttgtatctggatacaaaaataaactttttgttatatttctgat------taaatgtagGTTGGTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATG
||| | | || |||| || | | || | | ||| | || ||| || ||| | | ||| | | || | | | | |||||||| ||| | |||||||| || ||||| || || || ||||||||||||||||| || || |||||||||||||||||||| ||||| ||||| ||||
gaacttctgggatagttgatgttattattttttttccccgagt----cttatgactaaatataat--taagcatcttggtctgctttgggtattttatgatcttagGTTGGCAACAGGTCTAGTGAGTTCCATCCAGAGGTGAGAAGAGTGAGGCGTGAAGGGTCATATATTTACGAGGAGTTCATGCCAACTGGAGGGACAGATG
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 5
-gaaaccaaacaacattttc-tgttcttcatgtattcttatgtatttttcttgtatctggatacaaaaataaactttttgttatatttctgattaaatgtagGTTGGTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATG
| | | || |||| | || | || | || | | || | || || | | | | || | || | |||||||| ||| | |||||||| || ||||| || || || ||||||||||||||||| || || |||||||||||||||||||| ||||| ||||| ||||
acttctgggatagtacgttgatgttatcaatttttttccgaatcttatgactaaatataattaagcaacttggtctgctttgggtatttt--ttgatcttagGTTGGCAACAGGTCTAGTGAGTTCCATCCAGAGGTGAGAAGAGTGAGGCGTGAAGGGTCCTATATTTACGAGGAGTTCATGCCAACTGGAGGGACAGATG
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 7
gaaaccaaacaacattttctgttcttcatgtattcttatgtatttttcttgtatctggatacaaaaataaactttttgttatat-ttctg---attaaatg----tagGTTGGTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATG
| |||| ||| | | | || ||| ||| || || || ||| | || ||| | ||| ||| | || || ||||||| |||||||| || | || ||||||||||| || || || || |||||||||||||||||||| || ||||| ||||| || ||||| ||||| ||||| ||||
-------atttctggtttcccttccac-tcttttattagttatattactgatagtctgatgtataattaatcaacttggtatctgttttgggtattaaattatcttagGTTGGCAATAGGTCCAGTGAATTTCACCCAGAAGTGAGAAGAGTGAGGCGTGAAGGATCCTATATTTATGAGGAATTTATGCCAACTGGAGGGACAGATG
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------gaaaccaaacaacattttctgttcttcatgtattcttatgtatttttcttgtatctggatacaaaaataaactttttgttatatttctgattaaatgtagGTTGGTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATG
| | ||| | ||||| | || || | | || | || || ||| | ||| | | | | | | | | || |||| |||||||| ||||||||||||||||| ||||| || || ||| | ||||| ||||| || ||||||||||| ||| | || || || || ||||
gtactgcatccttctgcagaacttctctgttctggatcgaactggttattctgatattgtcataattctgattagctccttttcttcctaatata----------tttcgct-tgtccccatcttactacagATTGGGAACCGATCAAGTGAATTTCATCCTGACGTCAGAAGGGTAAGGAGAGAAGGCTCTTATATATACGAGGAGTTTATGGCCACCGGAGGAACTGATG
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 8
gaaaccaaacaacattttctgttcttcatgtattcttatgtatttttcttgtatctggatacaaaaataaactttttgttatatttctgattaaatgt-agGTTGGTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATG
| | | || | | |||| | | || |||| | || | | | | | || || | || || | | ||||||| || ||||| ||||| ||||||||||||||||| ||||| ||| | ||||| ||||| || || |||||||| ||||||||||| || || ||||
cttctcggattgaacattttagt-ttcaaatgattgtaataatttgtggcacatttctgtggttagcaatatttctttctgacccaatgtttttgttttagGTTGGGAATCGATCAAGTGAGTTTCATCCTGATGTCAGAAGAGTAAGGAGAGAAGGTTCTTATATATATGAGGAGTTTATGCCTACTGGGGGAACTGATG
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 7
-----gaaaccaaacaacattttctgttcttcatgtattcttatgtatttt-----tcttgtatctggatacaaaaataaactttttgttatatttctgattaaatgtagGTTGGTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATG
|| | | | ||| || | |||| | || || || |||| | || ||||| | ||| | ||||| |||| || ||||||||||||| || ||||| || ||||| || || || ||||||||||||||||| ||||| || || ||||| || ||||| ||||| || || ||||
cactagatttttagcttctattttcattgtaaatgtttgtccatacatcttatacttcttccgtgtgcatacacacatataatttttattattgtttc----------agGTTGGTAACCGCTCAAGTGAGTTCCATCCAGAGGTTAGAAGAGTGAGGCGTGAAGGCTCTTATATATATGAGGAATTTATGCCAACTGGAGGAACAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgtatctggatacaaaaataaactttttgttatatttctgattaaatgtagGTTGGTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATG
ttctgat putative branch site (score: 3)
atacaaaaataaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaaccaaacaacattttctgttcttcatgtattcttatgtatttttcttgtatctggatacaaaaataaactttttgttatatttctgattaaatgtagGTTGGTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
-aaaccaa
- - - - - - - - ttctgtt
- - - - - - - - - - - - - catgtat
- - - - - - - - - - - - - - - - -tcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctga