Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgatttatatattcctgtgccagccacagttgtggaaaagattatgccatgttacttatgtaatagctgataccagtaattaagaactgcagtatctcaggctaatttcataaaaccgtgtacctattgatcataatagatttggaacttatgcatcaaaacttattgcagTTGTCTAATGCTGGAGGACGGCTTGTCATTGCTAGCGATGGTGTCTGGGATGCACTGCGCTTTCAGGAAGCTCTGAACTATACCAGAGGACTGCCAGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g27780.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g27780.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G077960_T01 (Zea mays), 3'ss of exon 5
--gtatgtgatttatatattcctgtgccagccacagttgtggaaaagattatgccatgttacttatgtaatagctgataccagtaattaagaactgcagtatctcaggctaatttcataaaaccgtgtacctattgatcataatagatttggaacttatgcatcaaaacttattgcagTTGTCTAATGCTGGAGGACGGCTTGTCATTGCTAGCGATGGTGTCTGGGATGCACTGCGCTTTCAGGAAGCTCTGAACTATACCAGAGGACTGCCAGCTG
| || | | ||| | | | | || | ||||||||| || | ||||| ||| || | | || |||| | | || | ||||||||| ||| || || | | | ||||||| || || | | || |||||||||||||| |||||||| || |||||||||||||| || |||||||| ||||||||||||| |||||| || ||||||||||| ||||| || ||||||||||
gtgcatataacatatgaactatttatataagtgcaatggtggaaaaggttct-ttgtgtta-ttagatagtggtagagaccaatcacaaaaa----tggtatctcagcttaaggccactaatc--taaatgaattgatctg---aggttcgatgcctaca---------ttattgcagTTGTCCAATGCTGGTGGGCGGCTTGTCATTGCCAGTGATGGTGTGTGGGATGCACTGCACTTTCAAGAGGCTCTGAACTACACCAGGGGCCTGCCAGCTG
upper sequence: LOC_Os03g27780.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G150213_T05 (Zea mays), 3'ss of exon 5
--gtatgtgatttatatattcctgtgccagccacagttgtggaaaagattatgccatgttacttatgtaatagctg-ataccagtaattaagaactgcagtatctcaggctaatttcataaaaccgtgtacctattgatcataatagatttggaacttatgcatcaaaacttattgcagTTGTCTAATGCTGGAGGACGGCTTGTCATTGCTAGCGATGGTGTCTGGGATGCACTGCGCTTTCAGGAAGCTCTGAACTATACCAGAGGACTGCCAGCTG
| || || ||| | | | | | | |||||||||||| | ||||||| ||| || |||| | | |||| | || |||| | | ||||||||| ||| || | || | | | | ||| || || |||| | || |||||||||||||| |||||||| || |||||||||||||| || |||||||| |||||||| ||| | ||||| || ||||||||||| | ||| || || ||||| |
gtgcataacatatatgaactatttatataagtgtaatggtggaaaagattct-tcatgtta-ttagatagtagcaggagaccaatcataaagatcaacggtatctcagcataaggtc-tgtaatc-taaatgaactga---tacgaggtttgatgcctaca---------ttattgcagTTGTCCAATGCTGGTGGGCGGCTTGTCATTGCCAGTGATGGTGTGTGGGATGCGCTGTGTTTTCAAGAGGCTCTGAACTACATCAGGGGTCTACCAGCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtgtacctattgatcataatagatttggaacttatgcatcaaaacttattgcagTTGTCTAATGCTGGAGGACGGCTTGTCATTGCTAGCGATGGTGTCTGGGATGCACTGCGCTTTCAGGAAGCTCTGAACTATACCAGAGGACTGCCAGCTG
tattgat putative branch site (score: 3)
tattgatcataata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgatttatatattcctgtgccagccacagttgtggaaaagattatgccatgttacttatgtaatagctgataccagtaattaagaactgcagtatctcaggctaatttcataaaaccgtgtacctattgatcataatagatttggaacttatgcatcaaaacttattgcagTTGTCTAATGCTGGAGGACGGCTTGTCATTGCTAGCGATGGTGTCTGGGATGCACTGCGCTTTCAGGAAGCTCTGAACTATACCAGAGGACTGCCAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG