Sequence
atgc intronic sequence ATGC exonic sequencegttaactggctatctatagtgtttactgttttaatttaattattggcgtagtagtatctaataaaaatgattaaaaaaacattttctgttgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC
Basic information
species | Oryza sativa |
transcript | LOC_Os04g04950.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 5
gttaactggctatctatagtgtttactgttttaatttaattattggcgtagtagtatctaataaaa-atgattaaaaaaacattttctgt-----tgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC
|| || | || | || | ||| || || | | | ||| | || | | | || | |||||| | | |||||||||| || |||||||| ||||| || ||||||||||| ||| | |||||||||||||||||||||| | | ||| || | ||| | ||||| ||||
-gtagatgttaagttactatattgtttatttgtcattggaaat--gtgcaaagatatttgattcattgtaactactagtcttttttctttctcttttaacagTGGAATTTCCGTATTGGATTCACACCCAAAGAAGGTTTGGTTATATATTCTGTTGCATATGTTGATGGTAGTCATGGACGAAGGCCTGTTGCTCATAGGC
upper sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 5
gttaactggctatctata-gtgtttactgttttaatttaattattggcgtagtagtatctaataaaaatgattaaaaaaacattttctgttgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC
| || | |||| | ||| | || | | | | | | | | ||| || | | | | ||||| || |||||||| ||||||||||| ||||| |||| || ||||| ||| ||||||| || || ||| ||||||||| || || || |||| | || || ||
-gtggttgtttgtctaagtatattttccaaaacaacatcaatgt-atcatccttatcatgaattgctataactgattgacaattttttg-----cagTGGAATTTTCGTATTGGATTCACTCCTAGGGAGGGTTTGGTTATTCATTCAGTAGCCTATATTGATGGAAGTCGGGGACGGAGACCAGTGGCCCATAGAT
upper sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G09290.1 (Glycine max), 3'ss of exon 4
gttaactggctatctatagtgtttac-tgttttaatttaattattggcgtagtagt-atctaata----aaaatgattaaaaaaacattttctgttgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC
| | | | | | | | | ||| | || |||| ||||| | | | | | ||| | || | | | ||| || | || ||||||||||||||||||| ||||| |||| ||||||||| ||| | |||| ||||||||| ||||||| | | || || | ||| | || || || |
gatgatag--tgtaaaaaatctttccacattctaatcaaattaatttccgaatgtccaactagttctgtaactctgtcactatgttctttgctcattaatagTGGAACTTTCGTATTGGATTCACTCCTAGAGAAGGTTTGGTTATATATTCGGTTGCATATATTGATGGTAGTCAAGGGCGAAGGCCTGTAGCACATAGAC
upper sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G42490.1 (Arabidopsis thaliana), 3'ss of exon 5
gttaactggctatctatagtgtttactgttttaatttaattattggcgtagtagtatctaataaaaatgattaaaaaaacattttctgttgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC
| | | || | || || || || | | | || | | ||| || | || |||||| | | ||||||||||||||||||||| ||||| || | ||||||||||| | ||||| || |||||||||||||| | || || || | ||| | || |||||||
----gtagatttccagtaatagc--ctacttgaaaccaagtgattatgcttaagcttatttctaaattggctcaa----cattttgttt---acagTGGAACTTTCGTATTGGATTCACTCCAAGGGAAGGTTTAGTCATACATTCGGTAGCATATGTTGATGGCAGTCGAGGTCGAAGGCCTGTTGCACACAGGC
upper sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 5
---gttaactggctatctatagtgtttactgttttaatttaattattggcgtagtagtatctaataaaaatgattaaaaaaacattttctgttgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC
||| || | | | |||||| ||| ||| | | | | || ||| || | ||| | || || | |||||||| ||||||||||| |||||||| | ||| ||||| ||| || |||||||||||||| ||||||| | || || || || || | || || |||
gtgattacctttttgggaaagtaggttactggaa-aatctaagt-tcaacctgcta-tatggcttatcatctatttttatttttattcctcattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCTGTTGCATATATTGATGGTAGTCGAGGTCGAAGATCTGTGGCCCATAGGT
upper sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 5
gttaactggctatctatag-tgtttactgttttaatttaattattggcgtagtagtatctaataaaaatgattaaaaaaacat-tttctgttgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC
|| | | | ||| || || | | | ||| |||||| | | || | || |||| | || || || ||| || | |||||||| || |||||||| ||||| || | ||| ||||| ||| | ||||||||||||||||||||||| | || || || ||||| | ||||| |||
gtacttttggtttcttgagctggcttgttaataaatgtaattaaagtc--agagatgcatactaaacactatcaatgttttatctttttggttggcagTGGAATTTCCGTATTGGTTTCACTCCCAGAGAGGGTTTGGTTATCCATTCTGTTGCATATGTTGATGGTAGTCGGGGTCGAAGACCTGTAGCTCATAGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attggcgtagtagtatctaataaaaatgattaaaaaaacattttctgttgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC
atctaat putative branch site (score: 3)
ttttctgtt putative PPT
tagtagtatctaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaactggctatctatagtgtttactgttttaatttaattattggcgtagtagtatctaataaaaatgattaaaaaaacattttctgttgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA