RnoINT0040211 @ rn6
Intron Retention
Gene
ENSRNOG00000031782 | Col6a4
Description
collagen, type VI, alpha 4 [Source:RGD Symbol;Acc:1564060]
Coordinates
chr8:114696168-114697636:-
Coord C1 exon
chr8:114697601-114697636
Coord A exon
chr8:114696205-114697600
Coord C2 exon
chr8:114696168-114696204
Length
1396 bp
Sequences
Splice sites
5' ss Seq
ACGGTAGGT
5' ss Score
10.15
3' ss Seq
CTCTCCCCATCTCTCTACAGCCC
3' ss Score
11.02
Exon sequences
Seq C1 exon
GGCATCAAGGGCCCAAAAGGCTTGGCAGATAGGACG
Seq A exon
GTAGGTAAAGACTCCTAATTTGAAAATTCACTCATTTTAGAACATAAATCTTTCTATATCTACAGAGCTAGATTTGTTAATCTTAAAGCTTCTTAATTTTTCCTTTTATAAATTTTGTTAACACTTTAAGTTTATGGAGGTTTCCCCAGAAGTGCCACTATAAAATTAGAATAATATTTTAACCATTAAGTGACACAAAAGAAAATATTGGGGACCTACCTCCTTTCTGAAGAATGCTCTTTTGTAAAGCTAAAAACACTGGTTATAAAGCTATGTATTTTTTTTTAAATTGGGGCTGACTTACAGTTGCTTTTTTTTTTTTCTTTTCTTTCGGAGCTGGGGACCGAACCCAGGGCCTTGCGCTTGCTAGGCAAGCGCTCTACCACTGAGCTAAATCCCCAACCCCAAGCTATGTATTTTTAATAATGCCAATTCACCGAGTAGCACAGGTTTTCATGTCTTATGGGATACTCCAGAAATAATATCGGCAATGACAAGGAGTACTTTTCTCCCAAGTGCACAGACTGTTAGGTGGGGTTGCAGGAAGTGGAAACAACCAAAGAACAGGAAGTGGCAGGGTCTGAAGTCGAGGGGAGAACAAAGGAGGGACGGGTTTCTAACTTTCCCACCTGCTCCCTAGTTCCCCAAAAGTGACTCTGGGGTTCATTACTTATTAATAAAATATCTAGGCCTAAGGCTTGTTCCCTGACTAGCTCGTAAATTATATTAGACCATTTATACTATTCTATGTCTCCTTGGTTTCATGCGTCCAGCTTCCTCTAAGTTCTGGTAGGGAATCCTCCTACCTGACGTATTGCGATTCCCTGCTCTTGCCAGATGTCCCACCTTTGAATCCTGACTCGGTTTATTGGCCATTAGATGTTTATTGGAAAAGATGCTTCCACACAGCGCACAAGAAATTATCCCTATAAGGGATAAAAAAACAAACAAACAACAAACAAAACAAACAACAAAGAGGTAGAATTCAGGGATCGGGCTATGGAGGATTTGTCTTGGTCGTCATTCTAAAGAAGTCTAGCAAACACTTCTATAAAAATGCATAAATTGACAGCAGTCCCCAGTATTCTCTCCTGAGATTCCTAGATTTCAACCTTCAGCATCAGAGTTGATCCCCTTGATTTACGAGGCAGACTACAAAGTAAAATGGTGTGCCCTACCTACCTATCTCAGTATCCCATCCTTTAAGTGTTTTAAAGTAGTGGCTGGATCTGGAAATAATATTGTTAGGTGGTATGATCAGCTCTGACAGGTTTGTGGTTTTCTGTTACATATTTAAATGCTTCAGCTAGTACACGTCATTACAAGTCAGGACAATGACATCTGCTCTGCATTAAATGCTTATTTCCTCTCCCTGCCTCTCCCCATCTCTCTACAG
Seq C2 exon
CCCTGTGAAATTGTTGATTTTGTGCGAGGAAACTGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031782:ENSRNOT00000047563:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(13.5=83.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]