RnoINT0039942 @ rn6
Intron Retention
Gene
ENSRNOG00000056772 | Col4a6
Description
collagen type IV alpha 6 chain [Source:RGD Symbol;Acc:1589724]
Coordinates
chrX:112407884-112408836:-
Coord C1 exon
chrX:112408645-112408836
Coord A exon
chrX:112407937-112408644
Coord C2 exon
chrX:112407884-112407936
Length
708 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
GCCCATATTCTCCTTTCCAGGAT
3' ss Score
10.04
Exon sequences
Seq C1 exon
GAGCTCCAGGAAATCAGGGCCCCATTGGGCAGCCTGGGATGCCTGGACACAGTGTGAGAGTGGGCTACACATTAGTAAAACACAGTCAGTCAGAACACGTGCCACCATGCCCCATTGGCATGAGCCAGCTATGGGTGGGTTACAGCTTGCTGTTCGTGGAAGGGCAGGAGAAAGCCCATAACCAGGATCTGG
Seq A exon
GTAAGTACTGGCTTTGACAGCTAGTCCACGCTCCATGTCCCTACAAGGATTGAGAACTGACCACTTTCTTCTCACAGCCCTTTAGACCTACGGTTGCAAAATAGGCCACAAGCATTAGCCCTGGAGTCAAAAGGATTGTGATCCAAATGCTGGTCCTACTGCTTCAAAGTCACATGCCCTGGGTAAATTATTCAATCTTTCCAAGCTTTCATCCTCCCTTAATGGGACTAAGCTATTTCTACTATCTGTCACATAGAGTGGTGTAAGGAATTCATGAATCACTCAATGTAAAATATATTTAAGCCTCCATTAAGTATTAGTGATTAGTGATAACAATAGTAACATGACCTGCAGGGCAGTGATGATTACCCAAGTATTAATTGCATTAGCAGCAGGTGTGCTAACTCTTAGACATGGATTCCATCCATTAAATGTTGGTTTTACAAAGCAGATTAATTAAGGAGTGATTATTCACTTTATCAAAAGATTCGTGTCATTATTCAACTCCCCTGGTACCTTTAGGATACAATTTGATCCTCAGACTCCAGCACCTACTAAAGTCACAGAACTGTGAGGAGAGAGCTATACTGCTCTGAGCAAGCATTTTAATGGAATTGACATCTTCGGGGGTGTGCTTGCCCAGGCCCTCGTGCCTCTGCTTTTTCGCCAGCACTTACCTGGGTCTTTGGCCCATATTCTCCTTTCCAG
Seq C2 exon
GATTTGGGCTGGGCTCCTGCCTGCCCCGATTCAGCCCCATGCCCTTCATTCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056772:ENSRNOT00000079180:41
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.477 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(38.3=35.4),PF0141314=C4=PU(40.6=66.2)
A:
NA
C2:
PF0141314=C4=FE(16.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGAAATCAGGGCCCCATTG
R:
TAGAATGAAGGGCATGGGGCT
Band lengths:
239-947
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]