RnoINT0039727 @ rn6
Intron Retention
Gene
ENSRNOG00000016281 | Col4a1
Description
collagen type IV alpha 1 chain [Source:RGD Symbol;Acc:1307148]
Coordinates
chr16:83609450-83609834:+
Coord C1 exon
chr16:83609450-83609617
Coord A exon
chr16:83609618-83609744
Coord C2 exon
chr16:83609745-83609834
Length
127 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
GACATTCCTTTTGACTGTAGGTT
3' ss Score
7.95
Exon sequences
Seq C1 exon
GTCCACCTGGAGTTAAAGGAGAGAAGGGATTCCCTGGATTCCCAGGACTGGATATGCCTGGCCCCAAAGGAGATAAAGGCTCTCAAGGACTTCCTGGCCTCACAGGACAGTCAGGGCTCCCTGGCCTCCCTGGACAGCAGGGGACTCCTGGAGTTCCAGGGTTCCCAG
Seq A exon
GTAAGTGACACCTGAGCTTTGCCCCAATCACTGGAGAGGAGGCATGGCTGACTTCCTTCTGACTCACGGGCATTTACCGCTGGAGGTCCACATATGGATGTGTTCTTGACATTCCTTTTGACTGTAG
Seq C2 exon
GTTCTAAAGGTGAAATGGGCGTCATGGGAACCCCGGGACAACCAGGCTCACCAGGACCAGCAGGCGCCCCAGGGTTACCCGGAGAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016281:ENSRNOT00000057386:32
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(30.5=31.6),PF0139113=Collagen=PU(62.9=68.4)
A:
NA
C2:
PF0139113=Collagen=PD(35.5=71.0),PF0139113=Collagen=PU(40.7=77.4)
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:
TCCACCTGGAGTTAAAGGAGAGA
R:
GTAACCCTGGGGCGCCTG
Band lengths:
245-372
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]