Sequence
atgc intronic sequence ATGC exonic sequence...acataaaaaaagttagattcattgatgctagaatgatgtaatataatcggttttcactaatgatttactgccaggggctgtttttattgtgctcgtatagTTTCTCTGCGGATACATGCGAAGAGATGGGCATGAAGATGGTGAAAGGAGTCAAGGAATAGAGGATTCTCTTATGTTTGGGCCAGACGATGATAATGGTT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g23680.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g23680.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 1
acataaaaaaagttagattcattgatgcta-gaatgatgtaatataatcggttttcactaatgatttactgccaggggctgtttttattgtgctcgtatagTTTCTCTGCGGATACATGCGAAGAGATGGGCATGAAGATGGTGAAAGGAGTCAAGGAATAGAGGATTCTCTTATGTTTGGGCCAGACGATGATAATGGTT
|| | | | || | | | | || || | |||| | |||||||||||||||||||||||||||| |||||||||||||||| |||||||| |||||| ||||||||||||||||||||||||||| || || || | |||||||| || | | || |||||||||||||||| |||||| ||
ctatttttttaaatgacctttttatttccacgtatactgcagtatatttggttttcactaatgatttactgccaggg-ctgtttttattgtgcttgtatagTTGCTCTGCAGATACATGCGAAGAGATGGGCATGAAGGTGATGTGAGCAATCAAGGAAGGGATGGTGCTGTTATGTTTGGGCCAGATGATGATGGTGTAA
upper sequence: LOC_Os01g23680.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G081653_T01 (Zea mays), 3'ss of exon 1
-------------------------acataaaaaaagttagattcattgatgcta-gaatgatgtaatataatcggttttcactaatgatttactgccaggggctgtttttattgtgctcgtatagTTTCTCTGCGGATACATGCGAAGAGATGGGCATGAAGATGGTGAAAGGAGTCAAGGAATAGAGGATTCTCTTATGTTTGGGCCAGACGATGATAATGGTT
|| | | | || | | | | || || | |||| | |||||||||||||||||||||||||||| |||||||||||||||| |||||||| |||||| ||||||||||||||||||||||||||| || || || | |||||||| || | | || |||||
attgactaatcgttatgggttcaacctatttttttaaatgacctttttatttccacgtatactgcagtatatttggttttcactaatgatttactgccagGG-CTGTTTTTATTGTGCTTGTATAGTTGCTCTGCAGATACATGCGAAGAGATGGGCATGAAGGTGATGTGAGCAATCAAGGAAGGGATGGTGCTGTTATG-------------------------
upper sequence: LOC_Os01g23680.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G59870.1 (Arabidopsis thaliana), 3'ss of exon 1
acataaaaaaagttagattcattgatgctagaatgatgtaatataatcgg-ttttcactaatgatttactgccaggggctgtttttat-tgtgct--cgtatagTTTCTCTGCGGATACATGCGAAGAGATGGGCATGAAGATGGTGAAAGGAGTCAAGGAATAGAGGATTCTCTTATGTTTGGGCCAGACGATGATAATGGTT
| | || | | | || ||| | ||| | | | | || ||||||||||||||||||| ||||||||| | ||| | |||| | ||||||| | | | | | | || | | | | ||| || || ||| | | || || ||||| |||| || || |
atgctcacaacataccaataatctatgt----gttatgaattgcatttgggttttcactaatgatttactcccaggggctctgtttctatgtgatgctgtatagTGCTTTCCTGAACAAACGAGAGATCAAGACGACGTGGATAGTTGGGTGAACAAAGAGGACAATGTGACTTGTAGGTTTGACTCAGATGAAGACACCACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcggttttcactaatgatttactgccaggggctgtttttattgtgctcgtatagTTTCTCTGCGGATACATGCGAAGAGATGGGCATGAAGATGGTGAAAGGAGTCAAGGAATAGAGGATTCTCTTATGTTTGGGCCAGACGATGATAATGGTT
cactaat putative branch site (score: 2)
taatgattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acataaaaaaagttagattcattgatgctagaatgatgtaatataatcggttttcactaatgatttactgccaggggctgtttttattgtgctcgtatagTTTCTCTGCGGATACATGCGAAGAGATGGGCATGAAGATGGTGAAAGGAGTCAAGGAATAGAGGATTCTCTTATGTTTGGGCCAGACGATGATAATGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - aaaaaaa
- - - - - - - - - - - tgatgct
- - - - - - - - - - - - - - - - atgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggctg