RnoINT0039048 @ rn6
Intron Retention
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148266997-148268059:+
Coord C1 exon
chr5:148266997-148267023
Coord A exon
chr5:148267024-148267996
Coord C2 exon
chr5:148267997-148268059
Length
973 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CATTCTGGTTTTACCCACAGGGA
3' ss Score
10.44
Exon sequences
Seq C1 exon
GTCACACTTGGTCCCCCTGGCCTCAAG
Seq A exon
GTAAGACCTAGAAGAGAACAGAATTCTCATCTTCCTTGGTGACCTTGGTCCTTCCCACCTTGTGAGCCTCTATAGTACTGTGTTTATAGCAGGACTACTCCAGTGTGCTTAAGCACGTGTTGGAACCAGTGGGTTGTGTGTATAGGGTCCAGAGCTACCCTCTGCTGAGACCCTCTGTGTACCAGGTCTTGTGCCCTGTGACCCATCCTAAAAGGCAAGTGCTCCCCTTGAGCGTCAGGGGAGACTGAGGACTCATTGTGTCAGTCATAGGTTGGAGTGATCGTGTGTGGGTGTACCTGTATGTTCTGGAACACATGTCTGTGCCCATGTGACCACAGGCTGAATGTTGAACCCATATACACCTGCGGGCCTCATGGGCCCCAAGCTTGTGAGTGACGGGTGGGCATGGCTCATGTAGGCGAATGCCGTGCTTCCTTTGCCCGCTGTGAGCGTGCGGGCTCTGCCGGTTGTGGTGCCTACGGCACCCCCTGTCTGCTTTGCTTCTGTCTGGAGACGGCCATTGCATCCATTCTACCTTTATTGGTGAAGAATCAGGGAGGTGACCTGACTCTGCCCCGAGTCCTGTGGTAGCAAGCACAAGGCTTGAGCTCAGGAGACCTGACAATTAGCTGTCATGGGTTTATGTCATCCCGAGGGTCTATGCAGCATGTTCACGTGCCGAGGACATGCTGTGTGTTTGCTAATGTGAATGCCTGTGGGTGTGGGGGAGGGGATACTCCCTGTGTGAGACCCCTTCCCATGCGCCATGTGTGATAAGTGCACGGTGGGGGAGGGGGTAGGAGGAGGGAGTGTGTGTGTGAATGTGTGAGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTGCACTTGCATATTAGGTGGGTGGAGGCAACCAGGAGTGGGGAGCACTTTTTGGAGGCTCCCTTGAGGCACAGTCATCATTCTGGTTTTACCCACAG
Seq C2 exon
GGAGGGAAAGGTGACCAAGGCCTGACTGGACCATCAGGCCCCAAGGGAGAGAAGGGAGCACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475:ENSRNOT00000067663:12
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=FE(21.6=100)
A:
NA
C2:
PF0139113=Collagen=FE(54.1=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]