HsaINT0038025 @ hg19
Intron Retention
Gene
ENSG00000197467 | COL13A1
Description
collagen, type XIII, alpha 1 [Source:HGNC Symbol;Acc:2190]
Coordinates
chr10:71658453-71662611:+
Coord C1 exon
chr10:71658453-71658518
Coord A exon
chr10:71658519-71662503
Coord C2 exon
chr10:71662504-71662611
Length
3985 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAC
5' ss Score
6.89
3' ss Seq
TTCGTTTCCATGAACCTCAGGGC
3' ss Score
5.48
Exon sequences
Seq C1 exon
CTGCTGCCTCTCCTCAATTCAGTGCGACTGGCTCCACCCCCGGTCATAAAAAGGCGGACGTTCCAG
Seq A exon
GTAGACACCTCCCGTTTGTCCAGACCATGTGTGGTTTCCCAAGGGGCCCGGCAAGCCTGCTGGGGCTGCAGACAAAGCCAGAACCTCTCTCTAATTCAGTGAAATTAAATCAGACAAAAATAGGCCCACGTATACCATAGACATGGAAATACACAACACACAGGCCCCAGAAGACCCACAACTACCACCACACAATGATTACTCAAAACAGCCATCAACAAGAGCTGTCAGTGTGTGCCAGGCACCCTGTTACCCATTTCACAGGCCTGGTTATATTTCATTCACCAACAGTTTTATGAATTAGGCATGATCATCCTTATTTCACGATGAGGAAATCGAGGCTCAGAGAGGTTAACCAAGTTGCCAAGGTCACACAGCCAGTACATTGCAGAGTGGGGATTTGTACCCAGTCTCTCTGCCTGTTACTAGCTGTGTCATTTGGGGCAAGTTACTTGACCTGTGTCCCAGCCTTCTCATCTATAAAATAAGGATAATAACAGTGTCTATTTCACAGGGTTGTTGTTGATATGTAAAGCATTTGGAATAGTTCCTGGCACAGTTTAAGAGACATAATTGTTAGCTGTTTTTATTACTATTATCCATATTTTGGAGATAAGGTAACTGAGGCTCAGAGAAGTGAATTGATTTGCCCAAGGTTATACTAACAGTAAGAGGCAGAATTGAAACTGGCCTTGAAGCAGAATTGAAATTGAAGTCAGGTCTTCAGACCTCACATCCAGGGCTCTCTCAGCTGGACCTACCTCCTCTCTACTTAGAAATGCAGACTGCTTAGCATCTGATCCCTCGTAACCTGAGTTTGGGGAGCAAGGGAATTTGTGGAGGGAATGTAGTCCACAACCCACATTGTGAGCAAGTGCTTCCTTCTTCTTCCTGCCTTCCTAACCCAAGGAGGCTTGGATAGGAGCAGATCACAAAGAACAAAGCCATCTGGCCTCTGCTCTTCAGAGATCACAGCTTGATTCCAGGCTGGCTGGCCCATGGCTGCCCCTGTGCTCCTCACCTTTCTCATGCTGCACCAGGTACCCCGCCCAGCACAGGGACGCTAGCAGTGGCAGGGCTCTGAGCTGCTTTCTACAAGCCTGACCGCAGAGCCTCAAGCAACAATCTGGCCTGACTCAGGAGTCAGGAGCCCAAGGGCCTAGATGTTCAGGCACCTGATTGAACAAGGCTGAAAAATCCCTCCAATTAACAGCTAAAAATACAGAGGGACACGTGACTCCAGTGCCACCCAAGCCTGCAGGCCACATATCTCATTACGCCTGGCCAAATCCTCGAGAGCCTCCGTGTGCCCGAGCACTCACCAGAGCATGGCTACTCAGGAGGCCCACTGGCAGCTTAGAGAAGTACCAGGCCCACCCCTGTCACCCACCCCAGGCTGTGCCGGACCCCATTCCAGGAGAGCTGAGTCCACACTCTCAGAATAGCCATTCTCCTGGGCCCCAACAGCGACCTCCCAGCCTTAGGTGTATCAGCTGTTCTTTTTTGAGCCCTCACTGGGTTCCAGACATTGTTGTGAGAATTCTATGCAAATTATCTCATGCATTCCCCACACCAGCCATCTCACTATCCCCCGCTTTACAAAGGAAGAACTCAAGAGGGGTGCAGGATTCCATCCAGGCCACTGCATGTTACTGCCTCCCTTTTCAAGAGCAAGAGGTGGTGAAGCCAGAACTTTCTGTGCTACCCTGACCTGGTTTCCAAAGTAGAGAAAGAAGACGAGGCACCTCTGAGCTACCTGCTGCAGATTCTGCCTCCAGAATCAGGTTTTTTATGCTGTCAGCCACTATGGGACATAAAAATGCTTGTCCATTTCTTATCAATAAACCAATATTGATTTTACAGGCTCTACAAGCCGCTTAAACATTGGGTCTAAGATTCACTGAAAAAGGAAGCTTTATATGAAATATGATGTGCTTAGCAGATGGTGTTGGACGTCATTTCCAAAGAGCAGAAAGTGTAGATGGTGAGCCCTTTTTGCTGGGGGCTTACTTGGAAAGAATAGGGAGAGTCTGCAGTTCCAACTTTGGGTCCTGGCGCCACCCTGAATTCCCATGTGACTTTGATCAGAGAATTCAACTTCTTGGAGCCTCAGTTTTCTCTTCTGTAACATAGGACTTGTGACGTTATGAAGATTCTAGAATTTCACAGCCAGAAAGGAGCTCGGGAGTTTACTTCAGACTAAGCCTCCCCCATCTTGTGAATGTAGAAACCCACAAAAAATATAAACACACAAAGTACAGGATTCTGAGGAGGTTCCGGGACCCAAGCAGCTGAATCAGATTTGATGTGGTTGAAAAGGAGGCTGCACTGGTCCCTTTTTAAGGCCTGAGGCTTAGTGAAGCCTTTCTTGGTTCAGAAGAAACACTGACACCTGAGACTTATCAACAACCAACATGCAGCCGGGTGGGGGACCTGCAGTCAGGGCAGCTGCCACAGTGATTTCAACACCTGCTCCTCTGCCATGGACACCCTGAGCCCTAAAGTGGCTTCTCAGAGGGTGTGGCAGGATAGGACCCAGGCTCCAGAGTGACACTGCTAGATGCCATCTGCCTACAGGTTTTCCAGCCAAAAGATGGTGCAAGCAGGTCTTGCTGAAAGCTTACATTTCTCATTCCCAGGTTGTGCACTCCTATTTATCACCACCACTTCCCTCTAGAGTTTGCAGCAAGCATCATCAGCTGCCTTCCTCGCATGGGGAAGCAGGAGACCCCTCAGGTGTGTCATAGGGGCTTGCTGAGATCCTCTGAGAAAGGTGGGCCGGCCTGGAACTCCAGCCGCCTGCATCCCCCAGCCTCCACCCTAGAGCTCCCACACCTGCCAGGAGGTTCTGCTTCAGCCCATCTGCAGGGATGGGCCCCTCCTCACAAGAGCTAAGCCCAGATTGATCCCAGAGAGGTCATTTAGAAAATAACAAACCAAGGAGCCAGACTTGGTTTAGATCTAAGATGACTTTGTGTTGCCCCAGCCCTGAAATCTGGGTCACGTGCACCAGGCCATCTCCTCCTCCAGGGGGAGCATGATGCCATCGCTACCTCCCTGGGCTCACAGTCCATCCCGTGGACAGGCATGGTGGGAAGGCGGGCTCAGAGCAGCTGGCTGAGGAGACAAGGGAATAATAACAGCCTCCCCACGCAGCATAAAGCACTTCCACACAGCTTCCAAACTCTTTCAATGAAACCAAAGATTGCAGGCTCAATTGCCCTCCCAGGCCAGGCAGATCACCTTAAGTAACAGAAGCAGGCTGTGTGTGAGAAGGGCTAGGAGGGAGAGGACAAAAGCAGCCAGAGAACTCAGGCCCCACTTAACAGGCAGCCACTCCTTGGACGTAGGAATGTGGGCCCAGCTCAGCCAGGGTTCCCAGTGTTTCATCAGAAGCCACCAATTCAAATTTTATATGTAAAGTCTCTTGCTCAGTTGTTTAGTGAGCCAAATAAAATTCCATGGGCTTTGACCTAAGGATCCCATTTGATCCTCTGGGTCAGATAAAGACAGCAAAAAGCTGAGACAGGAAACGAGGGCTATTGTTCCCATTCTATGGCTGAGAGACTGGGGCTTAGGGAGAACTGTGCCTCGCCACACAGGGAGGGTGACAGAGGCAGGCCCAGGCTGAAGATTCAGGCCATCTGGCCAGGCTGGGAGCAGGCCTTTGGTTGGGCCAGGGGCTGTCTCCCACCCACTCCTCTGCCTCTGCCCCCCCGCAGAATGTCTCTCCGCAGCAACTCCTCTTTGGAAGCCCCACCTTCAGGGACCTAACATCTTGGCGTTCTTCTCACTGCCACCAGCCCCTGCATGTCATCACCACTACCACAGCATCATCACCATCATGCCACCGCTTCCTCCCCCCATCACCACTCCTTCCCGGCAGAAATCACAGCAGGCCTTCACTGGGTGCATGGCCTGAGGGTGGGGGACGGTCTGCAGCTCTGGGGGCCTTCCCTCTAACATTCGTTTCCATGAACCTCAG
Seq C2 exon
GGCGAACAGAGCCAGGCCAGCATCCAAGGTCCACCAGGGCCCCCAGGCCCCCCTGGACCAAGTGGACCTCTGGGGCACCCAGGACTGCCAGGGCCTATGGGGCCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197467-COL13A1:NM_080800:13
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.838 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(4.5=13.6)
A:
NA
C2:
PF0139113=Collagen=FE(53.0=100),PF0139113=Collagen=PU(19.6=30.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
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
- Genotype-Tissue Expression Project (GTEx)
- 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)