Sequence
atgc intronic sequence ATGC exonic sequence...gctatgctttacgtcgcgttttaatcttgtcgtggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g58740.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 3
gctatgctttacgtcgcgttttaatcttgtcgtggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaa-attttgttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
| | || | | | | | | ||| || | | | |||| || | ||||| ||||| ||| || |||| |||||||||||| || || ||||| || |||||||||||||||||||| ||||||||||| |||||||||||||| ||||| ||||| || |||||| |||||||
-gtgcagtgaactttattctatgcacatagcttggcgctcagtgacacccccaagtagcctatgatttcatcaatttgctgaacattctgatatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACTTTGCACTTTGCACATCTGAGATGATCTACATCACACACCTTCTGGAAGA
upper sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 2
-gctatgctttacgtcgcgttttaatcttgtcgtggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctg-cagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
| | | | | | | ||| | | || || | || || || ||||| | | | ||| | | || | || ||| |||| ||||| ||||| || |||||||||||||| || ||||||||||| |||||||| | ||||| || |||||||| | || || ||| | |||| ||
aagaaaggggttcaacatacctcta-cttttagaggcattcccatgtcttgctttctgatttataata-tataaatcctgtttttcattttaatgctgtcagGAATGGTAGCAGCCCTTACAAATGAGAGTGCCACAAGCAAATCCGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCACTTGTTGGCTGA
upper sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 2
---gctatgctttacgtcgcgttttaatcttgtcgtggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
| ||||| | | ||| |||| | | || ||| | || | || | || ||| | | | | || | | || |||| ||||| || ||| |||||||||||||||| |||||||| || || |||||||||| ||||||||||| ||||||| ||||| || || |||| |||
tctattgagctttgaattccttttctatctcaccatagtatattgcactcttaatattt--tcaattcttgtaatt-tgtactcacgaccttcaatttaacagGAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACTTTGCTCACTGCACATCTGAGATGATTTTTATAACTCATCTATTGGCAGA
upper sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G33340.1 (Glycine max), 3'ss of exon 3
---------------------------gctatgctttac--gtcgcgtttt----aatcttgtcgtggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
| | | |||| || || | | | | ||| || | | || || ||| | || | || | | | || |||| | |||| ||||| ||||| || || ||||||||||| ||||||||||| || |||||||| | |||||||| || |
aatgctaattcttgttctcttccttttgtttagtattactagtggcaaatgggaaagtttgactgtgacaataggaacctgccttgtttcatttccacagCTTACACTTATTT----TCTTATTATTGT-CAGGAATGGTAGCAGCCCTTACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACACTGCACATCAGAGA----------------------------
upper sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 2
gctatgctttacgtcgcgttttaatcttgtcgt--ggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
||| ||| | | || || | | |||| | | | ||||| | || | ||| | ||| | ||||| || |||| ||||| || ||| |||||||||| ||||| ||||||||||| || |||||||||| || || || || ||||||| || || || || |||| |||
ttgatgttttggactttttgattatttttctgccagttcatgagtcctctttttatatcgtcaagtcttaaactgtatttatttaatttca--atttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACTTTGCTCACTGTACTTCAGAGATGATTTTTATCACTCATCTATTGGCAGA
upper sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
gctatgctttacg-tcgcgttttaatct-tgtcgtggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
|| | | | | || ||| |||| | | | | | | || || ||| || || ||| || | | || |||| ||||| ||||||||||| ||||||||||| ||||||||||| || |||||||| | ||| ||||| || ||||||| || ||||| ||||| |||
gcattcttgtgtgatcctgttctaatttatatttccttttgaagaatattgagtttctgggttggaatttg--taagttcttactttgaatttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA
upper sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------------------------------------------------gctatgctttacgtcgcgttttaatcttgtcgtggtcatctgcctttttttt----tcttggtttatgcttctgttaattttctgaaattttg----ttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
|| ||| | | || | |||| | || | | | || ||| | ||| | | | || | || ||| | ||||| | || | |||| ||||| ||||| || || ||||||||||| ||||||||||| || |||||||| | ||| ||||| || ||||| | ||| || || | |||| ||
gtaagttgttatttctttatgatggtaatataatagagggatcattgtgcttgaagtttcatatatgagcatccttgtcagataaacttcagcaatgatctggttctcattttgacctactaggagaagaaaaccaaaatttaaaaatgttgttattggatttaatcaagagtctcacattttcactttgattttccagGAATGGTAGCAGCCCTGACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACATTGTACATCAGAGATGATCTTCATTACTCATTTGTTGGCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
tgttaat putative branch site (score: 3)
ttttgtt putative PPT
ttaattttctgaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctatgctttacgtcgcgttttaatcttgtcgtggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA