RnoINT0071193 @ rn6
Intron Retention
Gene
ENSRNOG00000028627 | Hmcn1
Description
hemicentin 1 [Source:RGD Symbol;Acc:1564772]
Coordinates
chr13:67933642-67934990:-
Coord C1 exon
chr13:67934853-67934990
Coord A exon
chr13:67933764-67934852
Coord C2 exon
chr13:67933642-67933763
Length
1089 bp
Sequences
Splice sites
5' ss Seq
CTGGTTAGT
5' ss Score
6.32
3' ss Seq
GAATGCCATGTCGTTCCCAGGAG
3' ss Score
6.52
Exon sequences
Seq C1 exon
GTCCAGCAATGAGAAAGATCATTTCTATCCTAAATCCCATTTACTGGACCACAGCAAAGGAAATAGGGGAAGCAGTCAATGGCTTTACCCTCACTAACGCAGTCTTCAAAAGAGAGACGCAAGTGGAATTTGCAACTG
Seq A exon
GTTAGTGTCAGATGAACGTAATATTCTACTAGATACATAGTTACAGACATATAGACAGAGAAGTCAGACAGAAAGACAGACCCACAGACACAGCTATAGATTGCCATACAGCTTGGTGACTAAGAAAAATACGGTGCATGCTTTCATGGAAAGTTATTACAAGTATTTGGTATACTCTTACACACATAATGGAAAACGGTTTTATATTTTCCTGTCAGTGAATGCTAGCACAAGGTTTGTAAGAAACCATGTGTCCTCAAGCAGAGCGGTAGTATTTATGCCCCAAAGATTCCTTTCTGTGCCTTCCTTTCTTTAAACCTTAGAGAGCATTTAAAACATGAATAAGGAAGGAAGATAAGTCATTCTTGTTATTAATTAAAGCTTTGTCTTTAACTGTGAATCAACCCATTTGTTTTACGGTGATTCTCTAACAGACGAGAGCAATGCTGACCACACTAACGCTTTCCACTCTTCTTCTGTCCTAATCATTGGGCGTCCCCTCTTTGGGGCCCTTCCAGTGCCCACAAAAGTGCTTACAAAGCTCCATTTCAGCCTCCTTGGGATGAGCCAGCCTTGGTACAATTGACCTTTGACCTTTGGTGAAGAATGATGAGGGAGGGTGTCTCCTTAACCAGCGTTTCATCAGCACAGAAAGCAAGTGGGCCTCTTGCTTTCTGTGCCATGTTCGAAGATGCCCTTTCAATATCGCCGAAGCTCAGGCAGAAACAAAACCCCGTAGCTAAGTCTGTGGGTATCGCCGGTCCCTGGTGAAGTTGCCTGGCCCATCTCACAAGCAGTGATTTTGTAGAAATACTTAATTATTCCTTGAGATTCTAAAATACGGGGTCTTCTGCCTAATCAAATGCTATACTTCCATTCTTCCTATGGCCACATAGAAAGACTTTGGGAAGACAGTTCAATAAGCCTGCCTTTTCTTAACTGGGAATCTTTCTCTGACATATTTATTCACATTTGAAATAGCATTATATTAGATCAGTCTTCTTGATCTAACCTTCCATAAATCATATGCATAACAGTAATAATGGCTTATTATCATCGCTGAGGAAATGAATGCCATGTCGTTCCCAG
Seq C2 exon
GAGAGGTCTTGAGGATGACACATGTGGCTCGGGGCTTAGATTCCGACGGCGCATTGCTGCTTGACGTCATTGTGAGTGGCCATGTCCTGCAGCTCCACTCACCTGCTGAAGTTAGTGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028627:ENSRNOT00000030971:96
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF074747=G2F=FE(24.5=100)
A:
NA
C2:
PF074747=G2F=FE(21.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCAGCAATGAGAAAGATCATTT
R:
ACTAACTTCAGCAGGTGAGTGG
Band lengths:
254-1343
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]