RnoINT0039047 @ rn6
Intron Retention
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148266047-148267023:+
Coord C1 exon
chr5:148266047-148266082
Coord A exon
chr5:148266083-148266996
Coord C2 exon
chr5:148266997-148267023
Length
914 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGT
5' ss Score
7.8
3' ss Seq
TCCTTCTTCTGTTCCCTTAGGTC
3' ss Score
12.12
Exon sequences
Seq C1 exon
TGTCCGCCCTGTGCCCGCAGCGCCCGGGAGAGCAAT
Seq A exon
GTGAGTGAATGAAGGAGCACAGCCAGTCTGGGAGTGGGTGTTGCCTGGAGTGGACTGGAGCTTCCTGGTAGAGGACAAGGGGGCTTTGTTCAATTTCCCATCACTCCCCTGCCTGTTTCCCAGAGCCGTGCTTGTCCCCACCCTTAAGCCCACCGAGCCAGGGCTGCCTTCTAGGCATTGAAATCTCAATGGAGTGTTGTGATCCAGAGTGGTGGCTTGCTTAGGGGATGGGGTGGGGTGGAGTACAGGACTCAAGACCTTGGTTGCTGGTTTCAGCTGTGCAGTTGCCCTCCAGGTCTTAGATCCACTTTGATTGGAAGGTACCATATGCCACCTTGGGGACTTAGAGCAGGGGAGGAACAGCCCAGTGCCACACAGCTCAGAGCCTGGGCATTCTCCTGTCCTCCTCGAAAGCTAGCCTAGCCCAGCCTTCCCACTGGGAGTTGGGAGGACAGGGTTCCATGAGCCGTTTGGTACCTACTGTGCCCCTTCTGTAGGCAGCAAGAGTTACCTTGTTTTCAGCTGTTGAGCTTCATCTATTCATAAAGGGCATGAACCCCCTAATTCTGGGGGGACTTAGAAGTACCCACACTTCTTCCTGCCTGCCTGCCTCTCATTCTCCCATCAAATCCCAGATGTGCTGGGGTTGCCATGGCAACCGAGTGACCATGTTAGCCTAACAATTTGAGGTGGGGCTGGCCAAAAGCAGGCAGGTTGGAGAAAGTCGACCCCTATGTTGGCTTTATTGCCTTGAAAAGCAGAGTACAGCATGCTAATTGGCCAAGGAGGCAGAGTTGGGGGTGGGACTCTGGCCCTGCCATCATGCTGTGTGAACCCAGCTGACTTGCTTGCTCTCTCTGGGCAGCTGGTTGCTCCCTAAAGTTAATATTCTCTTCCTTCTTCTGTTCCCTTAG
Seq C2 exon
GTCACACTTGGTCCCCCTGGCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475:ENSRNOT00000067663:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.905 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=FE(21.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]