RnoINT0039088 @ rn6
Intron Retention
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148292582-148294369:+
Coord C1 exon
chr5:148292582-148292626
Coord A exon
chr5:148292627-148294315
Coord C2 exon
chr5:148294316-148294369
Length
1689 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGA
5' ss Score
4.07
3' ss Seq
TCATGGTTTCTCTCTCTAAGGGT
3' ss Score
8.41
Exon sequences
Seq C1 exon
GGCCCCCCAGGTTTTCCTGGTGCTGTTGGCTCCCCCGGATTGCCT
Seq A exon
GTAAGAACCTAGCAGCACTCCGTCCCCTTTCCTGCCAGCCAGGTCTCTGTGGCTTCTGCTTGTCCCCCCTCCTGTTGTGCCACCTCCTCTACCCATTCCGTGTCCTGGTGTGCTGGTCATTGTCCCCCACCCCCACCCCCTGCAGGCATGGTAGCTAACGACACAGGGTCCCTTAAGTCTCCAGATTTGGCTCTCTGGTCTCTGACTTCTTTCTACGCTCCCTCAGCCGCTCCAGCACTCTTTTTCTCCTACCTTCATACCCTCCATTTTCCTTTTCCTTTCCCTCCAAGCCCACACGTCACTTCCCCTCTGCCCCCCAAAGCCTCTTTTACCTTCTGGCTGGAAGTTGGTGCCTCTAGAAAGGGAGCCACTTTATCTCTCCCGTCTCGCTCCTGCCTCCTGCTTCCCACCACGCTGTGTGGATTGAAGATTTGCTGAAAGTAGTCCTTGGGGCCCTGCCAGGCACCTGGCTCTGTGCCCAGCAGAGACGCCAAAGCTTTAGGGCTTCGCACTGCAGGCTGGCACAGGTCAGCCGCCCTGCTGCCTGGTAGGGCTGTCCAGAGGCGCTCTGGGGATTCACGGGCAGCTCTGTGTGCACCCTTCCCTGCAGCGAGAGGAAACCCAGGGCCTCCTCTTCGTCCCTCTTCCTTGGCTCCATGCCGAGTCTGCTCCAAGGCTGGGCATGTGGTGCCAGCCTGCTGGGTTTCTGGTGTTAGGGCCCTGCCCCACTGTGCCTAAGGCCTCAGGCTGATCCTTCTGCCAGGTGTCGTTAACTGCTCTGTCTTGTCACAGTCATTGTCACAGGTGTGTTTAAATCATAAACCCCCTCCCCATCCTCATTGTTGCTCTCTCCTGGGTCATGGAAGCTAAACCCCTTGTTTGTTGGATTTGTGTTTCCCGGGCTGCCTCCTGCCCTCCCAGGAGTGGTGGTTGAGGCCAGGGGCCAGGCATCCCCGCCCCCTGCCTTTGTCACATTTCCATCTGTTCCCACGTCTTCATCCCTGGCCGGACCATGTCTGTTTCTGCTTGCTTGGGTGAAGGGGCCATCTGTCTGTCTAGCCATCTGTCTTGTGTCATGGAGAGGTTTGGGTAGCACTTCTAGCAGGTACGAGGGAGAAGGGGGTGGCCGAGATGTCTTCAGTGTGGGAGCTGTGGAGGTCAGGGCGAGGAATGAGGGGCTTTGATCGAAACCCATGTCCCCATTCCCTGTTACTGAGTGACATGGAATTGTTCTGGAGAGAGCCCTCTTGTGCCTGTCCCTTGTATCCCTAAAGATGGTGATTTGCACTTGGGTGGGAACTGGGACAGGTAAGTGACATGGTGACACAGAACATCCTTTGCGGGGACACCTATCCTGATGGCCACCCGAAGGAGCACGCATGTCCCTAAAGGTGCATCCCAGACGGCCTCCACAGTGGGACACAGCAGCGTTGGTGACAGGGGTACCCTGTCTGCTGCTCACTGGAATTGTGTGTCTCTGCTGCTGCCTCTCTGGAAGCCATGCCCCTGAGAGGCATCCATATGTTTGGACTGTACCCTGGGTACACCACAGACAGTCACTCTGCCAGGGGCACTGGTTGCCACTTGTGACCTTCGTGCAGAATGGAAAGAGAGGCACATGGCAGGGAAGAGCCTGGGCTAGGTAGGGATTAACCTCCTCTGCGGTTTCTCATGGTTTCTCTCTCTAAG
Seq C2 exon
GGTCTTCAAGGGGAGCGAGGCCCCACAGGCCTGACTGGAGACAAGGGAGAACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475:ENSRNOT00000067663:49
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.789 A=NA C2=0.945
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(22.6=100),PF0139113=Collagen=PU(13.2=60.0)
A:
NA
C2:
PF0139113=Collagen=PD(3.2=11.1),PF0139113=Collagen=FE(25.0=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]