Sequence
atgc intronic sequence ATGC exonic sequence...caagcgtactaacttttaccatatacagaaattattatgaagtccttaaagtctctcactggctctttttagtagcttaacacttctacttgcttttcagGCAGCTTGTGATGATTTAAAAGGCAGTAGATTGTTCTTAAAACTCCTTGAAGCAGTGCTGAGGACAGGGAACAGAATGAATGTTGGCACAAACCGAGGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g20710.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g20710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G090693_T01 (Zea mays), 3'ss of exon 3
caagcgtactaacttttaccatatacagaaattattatgaagtccttaaagtctctcactggctctttttagtagct--taacact-tctacttgctttt-cagGCAGCTTGTGATGATTTAAAAGGCAGTAGATTGTTCTTAAAACTCCTTGAAGCAGTGCTGAGGACAGGGAACAGAATGAATGTTGGCACAAACCGAGGTG
|| | || ||| || ||| | | || || | | | | | | | || || | | | | || | || |||| |||| ||||||||||||||||||| |||||||||||||| | || || |||||||| || ||| | || |||||| |||||||||| ||||||||||| |||
---ttgttcctcctacccccacccacccaaaaaaaaacgatagccctgctctgaatta-tagtgcaaaaaaggagttgccattattgtcggcatggttttgcagGGAGCTTGTGATGATTTAAAAAGCAGTAGATTGTTCCTGAAGCTACTTGAAGCTGTCCTGCGAACTGGGAACCGAATGAATGTCGGCACAAACCGCGGTC
upper sequence: LOC_Os10g20710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G22410.1 (Glycine max), 3'ss of exon 3
------caagcgtactaacttttaccatatacagaaattattatgaagtccttaaagtctctcactggctctttttag--tagcttaacacttctacttgcttttcagGCAGCTTGTGATGATTTAAAAGGCAGTAGATTGTTCTTAAAACTCCTTGAAGCAGTGCTGAGGACAGGGAACAGAATGAATGTTGGCACAAACCGAGGTG
| || || | || | | ||| || || || | | | ||| ||| || | || | || || | | | ||||| || |||| || ||||| |||| | || ||| | ||||| |||||||| || || |||||||| ||||||||||||||||||||||| || ||||
gtatggctggcttatattcattcctttttatcttcaatgtttttgctttcaattgcattttgttctgcctccttaaaaactaatcaatcagttgttgatatctgtcagGTGGCAAGTGAGGAATTAAAGAACAGTCGGTTATTCCTCAAACTTCTTGAAGCTGTTCTAAGGACAGGAAACAGAATGAATGTTGGCACAAATCGCGGTG
upper sequence: LOC_Os10g20710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G40080.1 (Glycine max), 3'ss of exon 3
caagcgtactaacttttaccatatacagaaattattatgaagtccttaaagtctctcactggctctttttagtagcttaacacttctacttgcttttcagGCAGCTTGTGATGATTTAAAAGGCAGTAGATTGTTCTTAAAACTCCTTGAAGCAGTGCTGAGGACAGGGAACAGAATGAATGTTGGCACAAACCGAGGTG
| |||||| || | || | || || | | || || | | | | || | | || | | || || | | |||||||| || | || || |||| ||| | || ||| | |||||||||||||| || || |||||||| |||||||||||||||||||| || ||||| |
--gtctagctaactatttcaatg-attcaatcccttgtaa--tctttgatttatttatctcttccagaaaactaaccaatcagttgtgaatatctttcagGCTGCAAGCGAGGAAATAAAGAACAGCCGGTTATTCCTCAAACTCCTTGAAGCTGTTCTAAGGACAGGAAACAGAATGAATGTTGGCACTAATCGAGGGG
upper sequence: LOC_Os10g20710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G17460.1 (Glycine max), 3'ss of exon 3
--caagcgtactaacttttaccatatacagaaattattatgaagtccttaaa---gtctctcactggctctttttag--tagcttaacacttctacttgcttttcagGCAGCTTGTGATGATTTAAAAGGCAGTAGATTGTTCTTAAAACTCCTTGAAGCAGTGCTGAGGACAGGGAACAGAATGAATGTTGGCACAAACCGAGGTG
|| || | || | | | | | | | | || | | | ||| ||| || || || | | | | | | ||||||||| |||| || ||||| |||| | || ||| | ||||| |||||||| || || |||||||| ||||||||||||||||||||||| || ||||
gtatggctggcttatattcatcccttgatatcttcaatgtcttgcttttgattgcattttgttctgcctccttataaactaatcaatcggctgttgatatctgtcagGCAGCAAGTGAGGAATTAAAGAACAGTCGGTTATTCCTCAAACTTCTTGAAGCTGTTCTAAGGACAGGAAACAGAATGAATGTTGGCACAAATCGCGGTG
upper sequence: LOC_Os10g20710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G05220.1 (Glycine max), 3'ss of exon 3
-caagcgtactaacttttaccatatacagaaattattatgaagtccttaaagtctctcactggctctttttagtagcttaacacttctacttgcttttcagGCAGCTTGTGATGATTTAAAAGGCAGTAGATTGTTCTTAAAACTCCTTGAAGCAGTGCTGAGGACAGGGAACAGAATGAATGTTGGCACAAACCGAGGTG
| |||||| | || | || || | | || || | | | | || | | | || | | || || | || |||||||| || |||| || ||||| ||| | || ||| | |||||||||||||| || || |||||||| ||||||||||||||||| || |||||||| |
gtcttctagataacttatttcaatgattcaatcccttgtta--tctttgatttatttatct--cccaggaaactaaccaatcagttatgaatgtctttcagGCTGCAAGTGAGGAATTAAAGAACAGCCGGTTATTCCTCAAACTCCTTGAAGCTGTTCTAAGGACAGGAAACAGAATGAATGTTGGAACTAACCGAGGGG
upper sequence: LOC_Os10g20710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv07s0129g00220.t01 (Vitis vinifera), 3'ss of exon 3
caagcgtactaacttttaccatatacagaaattattatgaagtccttaaa-gtctctcactggctctttttagtag-cttaacacttctacttgcttttcagGCAGCTTGTGATGATTTAAAAGGCAGTAGATTGTTCTTAAAACTCCTTGAAGCAGTGCTGAGGACAGGGAACAGAATGAATGTTGGCACAAACCGAGGTG
| | || | | | | | | | | ||| || || || | | || || | || | | | | | | || ||||||||| |||| || || || ||| | ||||| | |||||||||||||| || || |||||||| || |||||||||||||||| ||| | ||||
--cctggaatagtgtagattagaaatggctacagatcaattgtctatacttgttccttaagagaactattcatgagacctcattatcttccaaatttgtcagGCAGCAAGTGAGGAATTGAAGAACAGCCGCCTGTTCCTTAAACTCCTTGAAGCTGTTCTCAGGACAGGAAATCGAATGAATGTTGGCACCAACAGGGGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaagtctctcactggctctttttagtagcttaacacttctacttgcttttcagGCAGCTTGTGATGATTTAAAAGGCAGTAGATTGTTCTTAAAACTCCTTGAAGCAGTGCTGAGGACAGGGAACAGAATGAATGTTGGCACAAACCGAGGTG
gcttaac putative branch site (score: 3)
cttctacttgcttttc CT-rich tract
tttttagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caagcgtactaacttttaccatatacagaaattattatgaagtccttaaagtctctcactggctctttttagtagcttaacacttctacttgcttttcagGCAGCTTGTGATGATTTAAAAGGCAGTAGATTGTTCTTAAAACTCCTTGAAGCAGTGCTGAGGACAGGGAACAGAATGAATGTTGGCACAAACCGAGGTG
- - - - - - - - - - - - acagaaa