BtaINT0021372 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002293 | ARL5A
Description
Bos taurus ADP-ribosylation factor-like 5A (ARL5A), mRNA. [Source:RefSeq mRNA;Acc:NM_001046245]
Coordinates
chr2:44480807-44482776:+
Coord C1 exon
chr2:44480807-44480954
Coord A exon
chr2:44480955-44482692
Coord C2 exon
chr2:44482693-44482776
Length
1738 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGT
5' ss Score
9.81
3' ss Seq
TTTTTTTGTAATTATTTTAGTTT
3' ss Score
8.16
Exon sequences
Seq C1 exon
TTCTATGAATGAAGTTGTGCATACATCCCCAACAATAGGAAGTAATGTAGAAGAGATAGTGATTAATAATACACGTTTTCTAATGTGGGATATCGGTGGCCAAGAATCTCTTCGTTCTTCCTGGAACACTTACTATACTAACACGGAG
Seq A exon
GTATGTTTCTTAATATACTAAGTCTTTTGTGAATATAATACTTGGGAAATACTTTCTAGATATAAACTCTTAAAGTTATCTTTTTGAAATATCACAGTATATTAATGTTAATATAAGTAGACTTTAAACATAATGGAATCTTTAATTCCCTCTTTCAGGGTCATTGTTCTGTATATCCAGTCTCATTGAACCGTAAGAAGAATTGGTGATTGATTAGTCTGATTTTATACTGATCCCAGAGCTTGTCTTAAATAATTGTTTTTCTAAAGAACTCCATTTCACAGTTTGTAACTTCATTTCTTTAGTACTATTTACTTGTGTCTGTATAGAGGAAATCCGAGTTAAATGAGGGGACTGGTGGTTTGAATCCTTGTTCAATAATTTTACTGTGTATTTTCTTTTATGCAATGCAATTGCACATTAAAGAACTCTTTTTATTATAAAACAGTTTAGATATAGTCATATGTTTTATTTACATATTATTTGCCAAGAGGAAATTTCTGACATTTGAGATCTTCACTGTATAGACCTTGTAAGATTAAAGGCTATGATATTTGTTTTTGTAGTGCTGGTTATAAGTTAATAAGTCTCCAACTGTATATATGGATGAGGCACTGTTAAATGTCTCTAATGACTTGATTCCCTAACACTCTGTTAAGAATTTGATCATGTCTTTTGTAGAAGGAGTATATATATGATTAGTATCCCCATATAAAATGCTGCATGTATTGTAAATTCATGCCATCGTCTTGAAAATCAATAGCTTTGTTGAAAGGTTTAGAGTAGGACATGTCTTAGAGCAATATAACCACATATCAGTAAAGTCTCAATGGGAGAAGAGGTCAAGTAGCAGTTCTCTTATCCATCTGCATTGTGGTTGATGAAATCTGAAGAATAGAGAAGATCCTGAAAATTAAGTGGTTTGTTTGGAAATGCTAGTTCTAAACAATATATAGTGCATACTAATACTAGGCAGTCAAAATTAACTTGGGCATAACCAGTGCCATCATAAAGTGACTATACCTGCTCCTGTTTCCCTGGTGCCTTTTGGTGCTCATGGAGTAGAAGGAGGGGCCATTGGAGCTCAGTCCTGCACAGCTCCTTTATGAGTGTTTGCATCTTCTGATGCTGGTCTCGTCAACAGTTCAGGAAAGAGCTGAACTGATTGTGCTTGCAGTAGCAGGGACCACTTATATAAGGAAGAAGGCATGGTTTTAGATACAGATTTATTCTTTAAATTTGTTGGGTTTTTTTTGAAAATTAACTCTCATATTACTTTATTCTCATACACCTGCCCTTTTAGATTTTTAAATTGACATTAATAAATAGTATCTGTCTAGAAGTAACTTAAATTTTGGGTCATAATATATTTTTGTCTTATGGACTTACAGTGCAAATAGAATTAAGATATTAGATATTAATTAAGATATTATAGAATTAAGATACTAATTTAGAAAACATGTTATATTTTGCTTAGTTTATTAGCAGAATATTCTAATAGAATGATGACATCATATTGTCTTTTATTTTCTCTTAAAAATTAGTAAATATGTTTGAATTAAAGATTAGACCTTTAGGCTTCACAAAGTATAGTGGGTATCTCTGGTTTTCAATAATACTATACCATAAGGTTCTAATTTCTTGATAGTTGTTAGACTGTAAATCAAATAAATACTTGATAAATTTTACAGATAGCAAATTATGTAATCACTAATGACTTTTTTTGTAATTATTTTAG
Seq C2 exon
TTTGTAATAGTTGTTGTGGACAGTACAGACAGAGAAAGGATTTCTGTAACTAGAGAAGAACTCTATAAAATGTTAGCCCATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002293:ENSBTAT00000002959:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002516=Arf=FE(28.5=100)
A:
NA
C2:
PF0002516=Arf=FE(15.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTATGAATGAAGTTGTGCATACATCC
R:
CTCATGGGCTAACATTTTATAGAGTT
Band lengths:
230-1968
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]