Sequence
atgc intronic sequence ATGC exonic sequence...gtctgtttatagaagaaaataatattgctactctctgataaatttcaataactattagtcttttaactgataaatgataagtactatttgcaatatgtagAGCGATGGGAGATGTTTCTGATCGCATTGGTCGCCCTACGGACAATGGACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g51480.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------gtctgtttatagaagaaaataatattgctactctctgataaatttcaat--aactattagt--------cttttaactgataaatgataagtactatttgcaatatgtagAGCGATGGGAGATGTTTCTGATCGCATTGGTCGCCCTACGGACAATGGACAG
|||| | || ||| |||| | | || |||| || | || || | | | |||| || |||| || | | |||| |||||||||||| ||||| |||||||||||||||||||| |||||||| ||||||||||||
gtttggacatgccatgacctttttactttactaagtatggatttatggttccacttaatgttgtccgtaggaaaacatatggtcattcagcgatatatgttgattgaaatgctggcgttccctatttttgtttggaaaataatggtt--tgtttgtaatatgtagAGCCATGGGTGATGTTTCTGATCGCATTGGCCGCCCTACTGACAATGGACAG
upper sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 4
gtctgttt-atagaagaaaataatattgctactctctgataaatttcaataact-attagtcttttaactg-ataaatgataa-gtactatttgcaatatgtagAGCGATGGGAGATGTTTCTGATCGCATTGGTCGCCCTACGGACAATGGACAG
| | || || ||| | | | | | | ||| || | || | ||| ||| | || || || || | || ||| | |||||||| ||||||||||| || ||||| || ||||| ||||| ||||||||||||
-ttggcttgattgaaaaccttgacactctaatatgtctatactttatgagaatttatttgtcacattcttgcatcaacaattccatgctcttttct---tgtagAGCAATGGGAGATGTCTCAGATCGTATAGGTCGTCCTACAGACAATGGACAG
upper sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S458_4V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------------gtctgtttatagaagaaaataatat-tgctactctc-------tgataaatttcaataacta--ttagtcttttaactga---taaatgataagtactatttgcaatatgtagAGCGATGGGAGATGTTTCTGATCGCATTGGTCGCCCTACGGACAATGGACAG
||| | | || ||| | ||||||| || | |||| | || ||| || | ||| ||| | | | || | | || |||||||||||||||||||||||||| |||||||| ||||| || |||||||||
gtaaaaatatggaccttcgtgatactgttcaatacttcagtaggtctaggtatttgggtgttggatcctacaaaacatgtctcaacttctcctctcataactcttcaatcccttctactcttcttgtgttggaagttttctagtggtagattaatcacaagattgaatcccaatcaaatggtataatggattcctgcagAGCGATGGGAGATGTTTCTGATCGAATTGGTCGACCTACAGATAATGGACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caataactattagtcttttaactgataaatgataagtactatttgcaatatgtagAGCGATGGGAGATGTTTCTGATCGCATTGGTCGCCCTACGGACAATGGACAG
ttttaactgataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtttatagaagaaaataatattgctactctctgataaatttcaataactattagtcttttaactgataaatgataagtactatttgcaatatgtagAGCGATGGGAGATGTTTCTGATCGCATTGGTCGCCCTACGGACAATGGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG