RnoINT0071129 @ rn6
Intron Retention
Gene
ENSRNOG00000028627 | Hmcn1
Description
hemicentin 1 [Source:RGD Symbol;Acc:1564772]
Coordinates
chr13:68064905-68066154:-
Coord C1 exon
chr13:68066053-68066154
Coord A exon
chr13:68065082-68066052
Coord C2 exon
chr13:68064905-68065081
Length
971 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
TTCTCGCCTTCTCCCTTCAGTTC
3' ss Score
10.53
Exon sequences
Seq C1 exon
AACCCCCCAGCCTGGATGATGGCGGGAAGATGCTGAACGAGAGCGTGGTGGTGAACAACCCCATTCAGCTGGAGTGTAAAGCCACAGGCAGTCCTGTTCCTG
Seq A exon
GTATGTTTACGTTGACTCTCTGCAACTGACTAACGCCTGATGTTTCTGAGCGTGGCAAGATCAGTATGAGTATAATATACCAGTTTGGAAGAAATAAAAGTGATAGAGTATACGTCAAGTGATATCCTCATTACTTAGAGCATATTTTTGAATGTTTAATAGCCTTTAAATGCATGAAAGAATTGTTCTACTTAGTGTACAAATATGCAAATGACTTAGCATCCTGTCTTTCTTGTGATCACAAAACTTATCAGGCTAATGTATGTCTGTGTATTTTGAAAAAATATTTGTATATTTTAAAGAGCATATTAGTGGTGATGAATAAACCAAGCTGCTCCTCAATCCTGGTCTTTCTCATGCTCCGGTCACTTTGGTCTACATCACTCTGTCACTTCTAGGCTATTCTTAACAATATGTAAAAATTATAGAATCCAGGATTGTGCATGGTAGATGGTTTTGACTTGACATGTCAACAATTTTGTAGGAAATGCACAATAAAGTAATGGGATAGGCTAAGAAATCTACCTTCAAGTACTATCGACATATTAGAAATAATACAAACAGTACTTTTGATTGGTTCAATTTCAGAACTCATTCGCTGGATTCAACAGTTTTCTTAGAATTATCATCTCTTAAAAATGGAGAGATGGCTCAGAGGTTAAGAGCACTTCCAGAGGTTCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTGTAATGGGATCCAATGAACTATTCCATTGTGTCTGAAGACAGCTACAGTGTACTCATATAAATAAAAATAAATAAAACAAAAACAAGAAGTCAACTCTCAAGAGATGTGCAGGACATTTTAACTCAAGGATTAAGTATAAGAATAGAGCATTATTTAGTTAGACACCTCTTAATATATTTACTTCAGATTCAACTTAGTTGATTGAATTTTGAGAGAAAATCTTTTACTTCTCGCCTTCTCCCTTCAG
Seq C2 exon
TTCTCACATGGTACAAAGACAGCCATCCACTCGCAGGCTCCACAAGTGCAACCTTCCTGAAGAGAGGGCAGATCCTTGAGATTGGAAGTGCTCAGATCTCAGATGCTGGCATCTACAAATGTGTAGCCATCAACTCTGCTGGAGCTACAGAATTGTTTTACAGCCTACAAGTTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028627:ENSRNOT00000030971:38
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.229 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(30.1=71.4)
A:
NA
C2:
PF0767911=I-set=PD(68.7=95.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCCAGCCTGGATGATGG
R:
CATGAACTTGTAGGCTGTAAAACA
Band lengths:
276-1247
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]