BtaINT0021380 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002035 | ARL5C
Description
ADP-ribosylation factor-like 5C [Source:HGNC Symbol;Acc:HGNC:31111]
Coordinates
chr19:40319250-40320137:+
Coord C1 exon
chr19:40319250-40319452
Coord A exon
chr19:40319453-40320076
Coord C2 exon
chr19:40320077-40320137
Length
624 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGA
5' ss Score
7.83
3' ss Seq
CTTCCCCCGGATGCTTCCAGAGC
3' ss Score
5.18
Exon sequences
Seq C1 exon
CCCAGGCCCCTTAGGGGACAGACTCGCGGGGCTTCAGGGACTTCATAGGTAAAGTTTGTGACAGCCTTCCCCAGGGGTAGGGGCTCCAAGCATCTGGGCTCGACCTGGGCCCCCGAAGACCCCCCGAGTCCTAGCCCTGTCTGACTCGGGACATGCCATGGGACAACTGATGGCCAAGTTGATGAGCATCTTCTGGGAACGGG
Seq A exon
GTAAGAGGCACATAAGTCATCCAAGTGACCACTTTGACCCAGCTCCCACCTGCTATCCGCCCCCTTTCCTCCCCCTCAACCTGTGGGGTGGTCTGGGAAGATGCGATGGGGCACGCTCAAATAATCCTGCGTGGGGGCTCCCTGCCTGCTCCGAAGTCTCCTCTGCCCCCTCCCGCCCACTCCTCGTCGGTCGCTCGCTTCGGTGCATCTTTGGGCGCCCCGCCCGGCGAGCCTCCTTCCTCGGGCTAAACGCGGTCGCCGGTTTCCTACGGTCGTGACTTCACGCTCAGCTCTTTCTTCAAACCCCTTCTCTTAACAAGAAGCCCTGGGTTCCCCGGACCTTTTGCACAATCATTTTTCTGGAAATGTGGAGAGGGGACAGTGGGGTTCAGCTCTCATTTCCGCTGTTCCGAGGTGGCTCAGGGGTCCCGTCCCGGTGGGAAAGAAATCTGTCCTGTTGGTTTCTTGTGTGGAGAGGGGGCTCGGGAGCAGAAGTAGTACCGTGAGCCGAGGTCCCCCAGCCTGCTGGGAACACATGTCTCCTTCCTTGGAGGCTGGTGGGGCACACAATCCCTTGGTCATCGGGTTTGGCCCTGACCCTGCCCTTCCCCCGGATGCTTCCAG
Seq C2 exon
AGCACAAGGTTATCATCGTGGGACTGGACAATGCAGGGAAGACCACCATTCTCTACCAGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002035:ENSBTAT00000002636:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002516=Arf=PU(8.8=78.9)
A:
NA
C2:
PF0002516=Arf=FE(11.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTAGGGGACAGACTCGCG
R:
CTGGTAGAGAATGGTGGTCTTCC
Band lengths:
254-878
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development