RnoINT0071130 @ rn6
Intron Retention
Gene
ENSRNOG00000028627 | Hmcn1
Description
hemicentin 1 [Source:RGD Symbol;Acc:1564772]
Coordinates
chr13:68063675-68065081:-
Coord C1 exon
chr13:68064905-68065081
Coord A exon
chr13:68063827-68064904
Coord C2 exon
chr13:68063675-68063826
Length
1078 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
TGTTTTCTTCCCCTTTATAGTGC
3' ss Score
9.9
Exon sequences
Seq C1 exon
TTCTCACATGGTACAAAGACAGCCATCCACTCGCAGGCTCCACAAGTGCAACCTTCCTGAAGAGAGGGCAGATCCTTGAGATTGGAAGTGCTCAGATCTCAGATGCTGGCATCTACAAATGTGTAGCCATCAACTCTGCTGGAGCTACAGAATTGTTTTACAGCCTACAAGTTCATG
Seq A exon
GTAAGTGCTTCAGCGCTCAGGTTCATACTGGGTAATGGCCACATAGGTAATGGCCACATGCTCTTATCAAACTATAATGTGGGTAAGCAATGGAACTATGCTATTAATAGTTTTACTTAAAGATCCGGTGCTCTAAAATTGGCAAACTTTCTTATCCCTGATATACTAAAAATGCCCAGGTTTCACACACTGTTGATTACTTTAGATTACTTGTTGAAATAATTAGTGATGGTTTTGTCAGCTAATAACAATACCATCTTTGCTAATGCAACTCATGGATATTAAAGGGGGGGAAATGATTTCAAGAGATATTGACAATTGGAATATAGCAGCATATGCAATCGAGAAGGTATGTGTGTACACACAAGTGCTCTCAATCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTCTCTCTCTCTCTGTGTGTCTCTCTCTGTGTGTGTTGTCTCTCTCTCTCGAATCAATAGTAAGAATTCACTCAGTGCCAGTGAGATAGCTCAACAGATATAAGCACTCTCTGAAACTGGGGGAAAAGTCTGATGTCCCCGTGCCCACTTGTTATCCCAGCACTCCTATGCCAAGACGGATGCTGGCAATAGGATCTCTCTGAAGCTCAGGGACCTGCTATCATGGAGTCCAGAGCCTGGCAGAAACAAGAGATTCCCTGACCCAACAAGGTAGAAGGAGAGAACAGACTCCCGCAAATGACCTTCACACATAGGTACATGCACAGACACACACACAGACACACACACAGACACACACACACACAAATAATAATAATAATAATAATAATAATAATAATAATAATAATATAATTTAAATGAACTCTGACATTGAAAACTGACCTCTTATAATAACTAGCAACATTTTCTTATCCTCCTGTGCCAAGCTGAGACACTGAAACTTGCTCTACATACTTCACAGGATACTGTGATTCGATCTCAGATAAGATATGAAACACTTAGTCAAAATAACAAGGAAGAAATTACCTTGTAAAAAGTACTAGGGAAATTAGTGGTTTTTCACTGTCCTGCGGTGACAACATTCATTATTGTTTTCTTCCCCTTTATAG
Seq C2 exon
TGCCTCCTTCGATCTCAGGGAGCAGTTCCATGGTGGAGGTGGTGGTGAACAATCTAGCAAGGTTAGAATGTGAAGCCAGGGGCATCCCTGCCCCCAGTCTGACCTGGTTGAAAGATGGGAGTCCAGTCTCTAGCTTCTCTAATGGAATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028627:ENSRNOT00000030971:39
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:
PF0767911=I-set=PD(68.7=95.0)
A:
NA
C2:
PF0767911=I-set=PU(53.9=94.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTACAAAGACAGCCATCCAC
R:
TGTATTCCATTAGAGAAGCTAGAGAC
Band lengths:
320-1398
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]