RnoINT0039749 @ rn6
Intron Retention
Gene
ENSRNOG00000016281 | Col4a1
Description
collagen type IV alpha 1 chain [Source:RGD Symbol;Acc:1307148]
Coordinates
chr16:83586287-83586822:+
Coord C1 exon
chr16:83586287-83586349
Coord A exon
chr16:83586350-83586768
Coord C2 exon
chr16:83586769-83586822
Length
419 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAC
5' ss Score
8.14
3' ss Seq
CATTTTTCCATCTTTCCCAGGGA
3' ss Score
9.36
Exon sequences
Seq C1 exon
GGTATTCCTGGCCAGGATGGTCCTCCAGGTCCCCCAGGTATCCCAGGATGCAATGGTACAAAG
Seq A exon
GTAAACTTAGACTCTCCCCTCCCTTGGGCATGTGCTTCTAGCTTTACACAGGACCAGTCACGGGGACATTCCTTATCTGGAAGCCTGCTTTCTTTGACAGGGAAAATGCAGCTTTTCACATTAAATATGTGGGAAAGATAACAGTTCCTTTCTACTTGTATGCTTTAGCCTAAAGTTGTTCTTTTAGAGATATTTTTTACCTGGAATTAATTACCAAATAGAACCTGCCACTCCGAGTCCTTATCTCTGTGAATCTTGCTGGGGAGTGAGGTGCTCCCTCAGTGAAGTGGCATTTAGGGTCTTGCTTATGACAGACCACACATGCTGACACCACTACAGTTTCTCTGGTGGGTGGGGACAATGATGGGCGGTGAAGTGTTGGGGTGCATTTGTGTGTGACATTTTTCCATCTTTCCCAG
Seq C2 exon
GGAGAGAGAGGGCCACTCGGTCCTCCTGGCTTGCCTGGATTCAGCGGGAATCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016281:ENSRNOT00000057386:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(17.0=71.4),PF0139113=Collagen=FE(33.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(28.3=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:
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]