HsaINT0038030 @ hg19
Intron Retention
Gene
ENSG00000197467 | COL13A1
Description
collagen, type XIII, alpha 1 [Source:HGNC Symbol;Acc:2190]
Coordinates
chr10:71678041-71678844:+
Coord C1 exon
chr10:71678041-71678073
Coord A exon
chr10:71678074-71678817
Coord C2 exon
chr10:71678818-71678844
Length
744 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
GTTTCTCTTTTTCCACACAGGGT
3' ss Score
9.82
Exon sequences
Seq C1 exon
GGGGCGCCCGGAATTGCCGTGGCTGGGATGAAG
Seq A exon
GTCAGTGGACTGTTGTAACCAACACATCAGGGACAGGGTGGGAGAGAAGAGAGCGGGCAGAGCTGGAAATCTTAGACTCAGTGGGGTGGCTGCCAGACCAATGAGGGGGCATACAGGATTTGGAAACATTTTTCTCAAAGTAACATTTGTGCCAGGTGCATAACCTTGAGCCACAGATGTGTAACTAAGCCTTGCAAGTAAGTAGCAATGGTTTCCTGCCTCAACTCACTAGCCTGCCAATGCACCAAGGCAGCAGGAAGGCAGCCCAGATCTTTCCTTTATGCTCTGTAATTGGGCAGCTATATGCTTCCAAAGCTTCAGAGAGAGCAGGAGTTCATCTCCAGAACCCCCACCCTAACTGCCCATTTGGTTGGCAGGCAGATGTGAGGACAGCCTGGAAAAACAAGTGCTCAAATTCTATCTTCACAGCAGGTGCACTTACAGGGGGCACCATGTCCAAACCAAATGTCCATTCCTTCCTCTCTTTCCTCCTGGGCTGCCTCACTTATGCTCCCACCTGCCACACCCCTCACCTGGGGAAGAATAGGACCCTCTAAGGGTCAGTAGCCTGATAGGCCTCCTTTGGCCTGGGACCTGATGCCTGAACAGAGAAGAGCCGGGGCTGGCCAGATGTTTCACTAACCCCACCCTGACTGCCCCCAACCCCACCTCCACCAACAGGTGCCTTGCTCATTTGTTTCTGCTTTTTCTGTCTCTCACATTTGTTTCTCTTTTTCCACACAG
Seq C2 exon
GGTGAGCCAGGGATCCCAGGAACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197467-COL13A1:NM_080800:18
Average complexity
IR-S
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=PD(12.5=63.6),PF0139113=Collagen=FE(15.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(4.8=33.3),PF0139113=Collagen=FE(12.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
ENSP00000346553, ENSP00000348695, ENSP00000350463, ENSP00000381936, ENSP00000381938, ENSP00000381940, ENSP00000381941, ENSP00000381943, ENSP00000381944, ENSP00000381945, ENSP00000381946, ENSP00000381949, ENSP00000381949f9775A, ENSP00000428057, ENSP00000428342, ENSP00000430061, ENSP00000430089, ENSP00000430173
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)