RnoINT0039559 @ rn6
Intron Retention
Gene
ENSRNOG00000007657 | Col27a1
Description
collagen type XXVII alpha 1 chain [Source:RGD Symbol;Acc:735115]
Coordinates
chr5:79164975-79165950:+
Coord C1 exon
chr5:79164975-79165040
Coord A exon
chr5:79165041-79165778
Coord C2 exon
chr5:79165779-79165950
Length
738 bp
Sequences
Splice sites
5' ss Seq
GAGGTACTG
5' ss Score
7.67
3' ss Seq
ATGGCCCTTTCTCTCTGTAGCAG
3' ss Score
9.1
Exon sequences
Seq C1 exon
CAACAAGATGACCTTGAGGCAGCTTTCCAAACGTGGATGGATGCTCACGGAGCAGTCAGATTGGAG
Seq A exon
GTACTGGCAGGATCTCTGCTCACATGACCTCTGGTCCTAGGAGAAAGAGAAAGGTCATAGCGGTTGATGCTATCCCCATGACTGGCACCAAGAGCATCAGAGACCTTCTCTCAGTGATGTCTCATGGTCTCAGATGGAGATCATCACTAGAAACCACAGTCCAAAGTGGTACTTCAGCCCACACTGCCAGAACCAGGCTAGACACAGACACTGCTTCCTAGCTTTTGTTGGAAGCGTCTGAGTCTATCGTGTGCTGGCCTGAGTCAGGGAGGGATGCTCATCTGACTCATAGCTCACAGAATGTCCCCAGGGTCACCCAGGGATTGCACAGAAGCAAGTGAGCCCCAGAGCTCTGCTGAGACCTGGTTTGTGGTCACCTCTGCTCCACAATTGCAGGCTGAGATGGGTCTTGGGTGATCTTTACTCCAGCCTGTATAAGAGCCTACTTTGCTGCTTTACATCCTTCTCCTGGTGGGGAGCTCACTCCCCTAGTTCAGACCTCCTACCAACCCTGCTGGGTTTCATAGACCAAGGGCAAGGAATCAGCTCTTGTCCCTGCTACATTCTGTCCCTGACCCTCCCTCTCCTTATCTGTTATAAGGCGGAGTAGCCAGTCTCAGTTAGCCATGAACTGGCTGGTCACCAGATCCCCAGACAGTGAGGATTTTAAAGCACTGTGTCTGGGACTTTGGGCAAGGCCCAAGCACTTAACAGGCCTATGGCCCTTTCTCTCTGTAG
Seq C2 exon
CAGGGGTACAGCTATCCGGACCAGCTGATGCTAGACCAGGGAGGGGAGATCTTCAAAACCTTACACTACCTCAGCAACCTCATCCAGAGCATTAAGACGCCCTTGGGCACCAAGGAGAACCCAGCCCGGGTCTGCCGGGACCTCATGGACTGCGAACAGAAGATGGCGGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007657:ENSRNOT00000010333:57
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.273 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0141013=COLFI=PU(38.6=46.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGACCTTGAGGCAGCTTTCC
R:
CATCCGCCATCTTCTGTTCGC
Band lengths:
231-969
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]