Sequence
atgc intronic sequence ATGC exonic sequencegtaaaataatctaaactaaaggtttttcagtcatatcttagcattaaattagatgagccaagcatgaacaaattcatctgtacttcatagctaactaacaatctttgtccatttccagATTCATATAATCTTCTGTGTGTGGGCAGCTGTGGCTCCTCCTTTTCCTTTCAAAGGAAAATCTTTGGCGTGAGTCTCCCCTATTCTTTTTCTTGTGTGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g42330.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 8
gtaaaataatctaaactaaaggtttttcagtcatatcttagcattaaattagatgagccaagcatgaacaaattcatctg--tacttcatagctaactaacaatctttgtccatttccagATTCATATAATCTTCTGTGTGTGGGCAGCTGTGGCTCCTCCTTTTCCTTTCAAAGGAAAATCTTTGGCGTGAGTCTCCCCTATTCTTTTTCTTGTGTGCA
|| | || | | | |||| | | | || | | |||| |||| ||| || ||| |||||||| | |||| ||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||
-----------------------------gtaagatgtc-gagtaaaataaacttaaggtttcacacattatgtcataaagttactgcatgactcactgccaatcttttccaattttcagATTCATATAATCTTCTGTGTCTGGGCAGCTGTGGCTCCTCCATTTCCTTTCAAAGGAAAATCTTTGGC--------------------------------
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 8
-------gtaaaataatctaaactaaaggtttttca-gtcatatcttagcattaaattagatgagccaagcatgaacaaattcatctgtacttcatagctaactaacaatctttgtccatttccagATTCATATAATCTTCTGTGTGTGGGCAGCTGTGGCTCCTCCTTTTCCTTTCAAAGGAAAATCTTTGGCGTGAGTCTCCCCTATTCTTTTTCTTGTGTGCA
|| | ||| |||||| ||||||| || |||| | || | ||| ||| ||| || ||| || ||| || ||| ||||||||| ||||||||||||||||||||| ||||||||||||||||||||||||||||| || |||||||||||||||||||||||
gtaagatgtcgagtaaaataaactgaaggtttcacacatcatgtatttgtattgtatt------------cataaagaaa----------ctgcatgcctcactgccaatctttgaccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC-------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaacaaattcatctgtacttcatagctaactaacaatctttgtccatttccagATTCATATAATCTTCTGTGTGTGGGCAGCTGTGGCTCCTCCTTTTCCTTTCAAAGGAAAATCTTTGGCGTGAGTCTCCCCTATTCTTTTTCTTGTGTGCA
aactaac putative branch site (score: 1)
tctttgtccatttcc putative PPT
aaattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaataatctaaactaaaggtttttcagtcatatcttagcattaaattagatgagccaagcatgaacaaattcatctgtacttcatagctaactaacaatctttgtccatttccagATTCATATAATCTTCTGTGTGTGGGCAGCTGTGGCTCCTCCTTTTCCTTTCAAAGGAAAATCTTTGGCGTGAGTCTCCCCTATTCTTTTTCTTGTGTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA