RnoINT0039107 @ rn6
Intron Retention
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148307015-148308003:+
Coord C1 exon
chr5:148307015-148307059
Coord A exon
chr5:148307060-148307814
Coord C2 exon
chr5:148307815-148308003
Length
755 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TGTACTGTGACCTGTCCTAGGGT
3' ss Score
6.35
Exon sequences
Seq C1 exon
GGACCTCCAGGAAAGCAGGGACTCTATGGACCCCCCGGCCCAAAG
Seq A exon
GTGAGGGGGCACTGGCTGGGTTTGGGAAGAGGTATTTGGGAACTCCAAGCTGCAACTTAGCCACAAAGGAGGCAGGCCTAGGGTGGCCAATGGGCAGGAAAGAGGGTGTGACCTCACCTGGGACTGTCCCATCTATGGCATGGAAATCTTTTTAATCCCCTACTCGCCCACTCTGGCTCACTCCAGGGCCCCTCTGTGTTGGTCTGGGGTAACCAGAAACCCTCCTACAACGACACTCCCTGTGCTTAGTCACCATGACACTGGAGTGCAGCAAATTTTGAGGAAGACTGGATACAGTGCTTCGAGACCCCAGGAAGTGAGGGAGGAAGACTGCACAAGGGGCAGGAATGTTTCCAGAGGACAGTAGAGGGGGACTCACTGGGGTGCCAAGGCTGGGGAGGGGCATTCCAGACAGCAGATTCAAGCAACATGGTGGAACCAGAGTGACAGGTAGCTAGAGCTGAGGAGACGAGGCTGAGGAAGGTATGAGGAAGACATTGTAATTGGTCTTGAATGAGTCAGGGGTACTTCCTACTGAGGGCATGTGGGAGCCAGGGGCATTTCCCAGCATTCCCAGTGATGCAAGCACTGCCTTCCAGAAGCACTGCTCTGGGAGTGCCGAGGCAGGGGGACCTGCATCATTGTGATTGTAGCCCCGGGGGAGATGCTGGGCACTTGGGGAAGGGGCAGGTTGCTGATACATTGTGACATAGACTTGGAAACAGTTGGTAATAGTGTACTGTGACCTGTCCTAG
Seq C2 exon
GGTGACCCAGGACCTGCAGGACAGAAAGGCCAAGCAGGAGAAAAGGGAAGATCTGGCATGCCTGGGGGCCCTGGCAAGAGTGGCTCCATGGGACCGATTGGACCACCGGGTCCTGCGGGAGAGAGAGGCCACCCTGGGTCCCCAGGGCCTGCTGGGAACCCTGGATTGCCTGGTTTGCCAGGCTCTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475:ENSRNOT00000067663:66
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:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCAGGAAAGCAGGGACTCT
R:
CATAGAGCCTGGCAAACCA
Band lengths:
230-985
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]