RnoINT0071166 @ rn6
Intron Retention
Gene
ENSRNOG00000028627 | Hmcn1
Description
hemicentin 1 [Source:RGD Symbol;Acc:1564772]
Coordinates
chr13:67979815-67981407:-
Coord C1 exon
chr13:67981326-67981407
Coord A exon
chr13:67979952-67981325
Coord C2 exon
chr13:67979815-67979951
Length
1374 bp
Sequences
Splice sites
5' ss Seq
ACGGTAACT
5' ss Score
7.53
3' ss Seq
TACGCTGTTCTCATGCTTAGTGC
3' ss Score
7.11
Exon sequences
Seq C1 exon
GTGGAGGACACAGGAAGATACACCTGCCTGGCATCCAGTCCTGCAGGGGACGATGATAAAGAATATCTAGTGAGAGTACACG
Seq A exon
GTAACTTTGGTGATTTATGTTGGAACCACATGCAATCCTAGTTAAAAACTGTACTAGAGAAGGTCCTGACATTTCACAGCACTTCATATGGAGATAAGTTGAGAAATGCATATTTTACAAATTTTATTCATTGTGTTAATAATGTATGAGCTCTTTGGGATATAGTTCATTGGAGTTTTGAGTTATTTGTCTTGTTTTCACCCAAACAATTCAAATTTGGTGACTTAAAAATAACAACATAAATTACAATAATGATTAGAATAAAAACAATCCATAGTCTTACCACACAAGGATACAATGTTTTTTTGTGTCTGTGAATATTTTATAGCTGAGCACAGCAGCATATATCTGTAGTCCCGGCTTCTTGGCAAGTTGAGGCAGGAAGATTGCTTAAGCTTAGGGAACTCATTAGGGAAATAAGAAGATCCTTACTATCAAAAAAAGGAACATTTCAGAACACAGAACTTAAGCCACTTTATGTCTCACTTAATGGCGTGATGAACACTCTTGTGTTAACACATATATTCCATAGCGTCATTTTAAGATTGCATGCTGCCATATATCTTACTCCCTTTTTAGAATTATTTAGACATATTAGGATAGTCTGCCTTTTTATCTATGTTGACAATATGTTAGCTATTTCCTTTATTTTTAAATTTTACTGTCCTACGCTGACTCGTTTCATATGCATGCATGTGCACATATGTCCTTTTAAAGATTTTTAAAATCATTGCCTTTTACTTTCCAGACAGTTTGAATTAACTAGGCCCTTTTGAATATTACTTTTATATATAAATTTAAATCACTCTTCATGGGGAGGAGTGTTTGAAAACCAAACAGAAATTGATCTAATTTTCAGTGCCTGACTGACTAGTCAATGCAGATCGTCTGGTATGAAGTTTCCCTGATATCCCTACTGAAAATTAAGGCCTACCTAAGTAAACCCAAATTATGATATACTGAGAAATATGTCTGTATTAATCAGGAAAAATGGACATTGTTCTTCATACTGCGATGGGCAGTTCCTTATTTGATCATTTTTCAGTAGTCAGAGTAAAGTATTACCCAGTGTGGAAGCTGATGGAAGGACAGCACTGTGCCTCTATTTCCTTACTACCCATCAAAGGTGACGATGGTGTAGTTATCTTATTATTCATGTGCTTTGCTGGAAAGATTCCATTATCTAATCAATAGGAAAGTGGTAAGTAATAAAGATCCAATTTGTTAATAATCTGGACCATACATTAGGTGACTAACCATTAAGGTCCATGCCTCCTTTATCGTCCCATAAACTTAGCCATTGTTGGAGACCAAATAGATCAATCATTTACAGCCCGTTTATCAAATGCACTGATACGCTGTTCTCATGCTTAG
Seq C2 exon
TGCCTCCTAACATTGCTGGAGTGGATGAAGCCCAGGACTTCACCGTGTTAAGGAACAGGCAGGTGACATTGGAATGCAAGTCCGACGCAGTGCCTCCACCTGTGATCATGTGGCTCAAAAATGGGGAGCAGTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028627:ENSRNOT00000030971:71
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.214 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(29.1=89.3)
A:
NA
C2:
PF0767911=I-set=PU(44.7=82.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACACAGGAAGATACACCTGC
R:
CTGTAACTGCTCCCCATTTTTGA
Band lengths:
214-1588
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]