RnoINT0071185 @ rn6
Intron Retention
Gene
ENSRNOG00000028627 | Hmcn1
Description
hemicentin 1 [Source:RGD Symbol;Acc:1564772]
Coordinates
chr13:67949849-67950322:-
Coord C1 exon
chr13:67950152-67950322
Coord A exon
chr13:67950020-67950151
Coord C2 exon
chr13:67949849-67950019
Length
132 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
ATGGTTTTACCTCCCTGTAGTGG
3' ss Score
6.6
Exon sequences
Seq C1 exon
TGCATGGTGGGTTTTCGTTGTGGTCTGCCTGGAGGTCCTGCAGTGTCACCTGTGGAAAAGGCATCCAAAAGAGGAGCAGGCTATGCAACAACCCTCCTCCAGCCAATGGAGGGAGGCCATGCCAAGGCTCAGAGTCAGAAGCACGACAGTGTCAAAATAAGTTGTGTCCAG
Seq A exon
GTATGTCTCTGCATTCAGTGAATAGGCATGTGTTTAATAGACACTAATTTATGTTCCTACCTTTGGCTGCCTCGTGGTCACTACTTGCCATTCGACTTTAGCTAATGATGTAATGGTTTTACCTCCCTGTAG
Seq C2 exon
TGGATGGTCACTGGTCAGAATGGAGCTTCTGGGAAGAATGCTCAAGAAGCTGTGGGCATGGCAACCAAACTAGGACGAGAACTTGCAGTAACCCACCGGCTCAGCATGGTGGGCGGCCATGTGAGGGGTATGCTGTGGAAACCATCATGTGTAACATTCGGCCTTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028627:ENSRNOT00000030971:89
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.103 A=NA C2=0.034
Domain overlap (PFAM):
C1:
PF0009014=TSP_1=WD(100=87.9)
A:
NA
C2:
PF0009014=TSP_1=WD(100=87.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCATGGTGGGTTTTCGTTGTG
R:
TCCTAGTTTGGTTGCCATGCC
Band lengths:
245-377
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]