HsaINT0023596 @ hg38
Intron Retention
Gene
ENSG00000154479 | CCDC173
Description
coiled-coil domain containing 173 [Source:HGNC Symbol;Acc:HGNC:25064]
Coordinates
chr2:169674576-169675040:-
Coord C1 exon
chr2:169674867-169675040
Coord A exon
chr2:169674770-169674866
Coord C2 exon
chr2:169674576-169674769
Length
97 bp
Sequences
Splice sites
5' ss Seq
CATGTACTA
5' ss Score
-4.29
3' ss Seq
CTATAATTTTTCTTTTGTAGTCG
3' ss Score
7.5
Exon sequences
Seq C1 exon
GGGATGAAAGAACAGAAACTTGAAGCCAAAAAGAAGCGTGATGAAGAAATAGAGGCAGAAAGACAAATTCTTGATCTGGAAGAAGAAATATACAAACAAGGAAAAAGAAAAAAGGCCATTGAAAATGCAAAGCAATATCAATTTTACCAGACAGAAAGAGTGAAAAACTTTCAT
Seq A exon
GTACTACTTGAGTTTTCTTGTATTTTTATATATCTTTAACATATCTGTACATAATTAGGCATCATTTCCTTAAAGTACTATAATTTTTCTTTTGTAG
Seq C2 exon
TCGGGACTTCTTCTTAGTAGAGTTATGAAAGAACGTGATGCCCAGATTGAATTCCGAAAGAGTAAGATAAAATCAGATAAAAAATGGGAGGAACAGTTGAAACTCAACATTGAAAAAGCTTTTAAAGAAGAACAAGAAAAAGCAGAAAAACGACACAGAGAAAGGGTGGCTCTTGCCAAAGATCATCTAAAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000154479:ENST00000447353:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.144 A=NA C2=0.258
Domain overlap (PFAM):
C1:
PF138681=Trichoplein=PU(2.7=15.5)
A:
NA
C2:
PF138681=Trichoplein=FE(19.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGCCATTGAAAATGCAAAGCA
R:
TGAGTTTCAACTGTTCCTCCCA
Band lengths:
168-265
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development