RnoINT0039087 @ rn6
Intron Retention
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148291787-148292626:+
Coord C1 exon
chr5:148291787-148291831
Coord A exon
chr5:148291832-148292581
Coord C2 exon
chr5:148292582-148292626
Length
750 bp
Sequences
Splice sites
5' ss Seq
GTTGTAAGT
5' ss Score
8.3
3' ss Seq
CTGCCTGTTTCTCCCACCAGGGC
3' ss Score
11.94
Exon sequences
Seq C1 exon
GGTCCACCTGGCATGAGGGGCTCTCCTGGTCTTCCAGGCCCTGTT
Seq A exon
GTAAGTATCTCTGGTATCCTGGTCTGTTTGAACAGGTCTCAGAAACTCCTAACCCACACACCACTCTGTAGCCAGGCAGGGACACCCACTGCCCTTACCTTCCCCTCATGAGAGCATTTTTTGGGGCTGTGGTCTCCTCCAACTTGGAATACCCTGAGGCACCCTGCTCTGCCCTCAGGGGCATGCGTTTGTGTCCCTCCTCCTCCCTGTTGCATTTAGTACCACACTAGGGACCCAGGTAGCCCCACAGCCAGCATGGTATCTAGTGCACAGCCAGATCTCTCCACTCACCTTAACACTCGTTCCTCCAAGGGTCTGGGATGGTGCCCTTCATAGCTCGGGGGCAGGGGGTCTCTAGGAAGTCTATAAGCACCAGGCTGGGGGTCTCTATCCAGAACCCACAGGGATGTTAGGGAAGCGGGAAAGATGTGACTAGAGAGATGAAAAGGGACAGTAATATGTTCTCTGGAGAAGAAAAATGGAGGCCATGGGGCTACTCGCCTGAGGGGCCTTGGTAGTCAGGTGGTGGGGCAGGGGTGCAAAACCAAAATGAAGCCATGGGGAGCCCTGGGAAGGGTTTCCTGGCTGGGAGGCTGCTGCTATCTCTGCCTGTGGAGGATCCTGCTTAGGGTCACAGTGGCCACCTTCTGCTAAGGTTCCTTCTCCGTGACCTCAAAAAAAAAACTCCCCGCCAAAGCTCCCCAGAGTGACTGCTCTTGTGAGATGTGACCTGCCTGTTTCTCCCACCAG
Seq C2 exon
GGCCCCCCAGGTTTTCCTGGTGCTGTTGGCTCCCCCGGATTGCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475:ENSRNOT00000067663:48
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.855 A=NA C2=0.789
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(14.0=37.5)
A:
NA
C2:
PF0139113=Collagen=FE(22.6=100),PF0139113=Collagen=PU(13.2=60.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
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]