HsaINT0038881 @ hg38
Intron Retention
Gene
ENSG00000168542 | COL3A1
Description
collagen type III alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2201]
Coordinates
chr2:188996398-188997218:+
Coord C1 exon
chr2:188996398-188996496
Coord A exon
chr2:188996497-188997164
Coord C2 exon
chr2:188997165-188997218
Length
668 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
ACCGACCACTTCTTCTTTAGGGT
3' ss Score
9.26
Exon sequences
Seq C1 exon
GGAAGTCAAGGAGAAAGTGGTCGACCAGGTCCTCCTGGGCCATCTGGTCCCCGAGGTCAGCCTGGTGTCATGGGCTTCCCCGGTCCTAAAGGAAATGAT
Seq A exon
GTGAGTTCCTTCATTAATTTCTTCAATAAATATTTGACTGGAAGGCTTTTATTTTCCATATGGAGTAAAGAAATGGTCAAAACTCAGTCTCCTCTTCAAAGCATGGAGGAGTATATGAAAATCAAATTGCATGTAGGAAGGGAGCTAAATATATAATTGGTTATGGTTGTATGTGTGTGTATGGAGCAGGCAGATAAAAAATATGAAACAGGCTGGGTGCGCTGGCTCACGCCTGTAATCCCAGCACTCTGGGAGGCCAAGGCAGGCAGATCACCTGAGGTCAGGAGTTCTAGGCCAGCCTTGCCAACATGGTGAAACCCTGTCTCCACTAAAAATACAAAAATTAGCCAGGCATGGTGGCATGTGCCTGTAATCCTAGCTACCCAGGAGGCTGAGGCAAGAGAATCACTAGAACCCGGGGGGCAGAGGCTACAGTGAGCCAAGATTGCGCCACTGCACTCCAGCCTGGGCGACAGAGCAAGACTCAGTCTCAAAAATATGTATGTGTGTGTGTGTATATATATATATGAGACATATATATATGAGACATATATATATGAGACATATATATATGAGACATATATATATGAGACATATATATATGAGACAATAATATGATTAGTTATTGCCCTTTGAGGATTAGTAAATACCGACCACTTCTTCTTTAG
Seq C2 exon
GGTGCTCCTGGTAAGAATGGAGAACGAGGTGGCCCTGGAGGACCTGGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168542:ENST00000304636:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(49.2=100),PF0139113=Collagen=PU(15.2=36.4)
A:
NA
C2:
PF0139113=Collagen=PD(8.2=27.8),PF0139113=Collagen=PU(23.4=83.3)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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