HsaINT0038025 @ hg38
Intron Retention
Gene
ENSG00000197467 | COL13A1
Description
collagen type XIII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2190]
Coordinates
chr10:69898697-69902855:+
Coord C1 exon
chr10:69898697-69898762
Coord A exon
chr10:69898763-69902747
Coord C2 exon
chr10:69902748-69902855
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:ENST00000398978:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.818 A=NA C2=0.977
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(4.4=13.6)
A:
NA
C2:
PF0139113=Collagen=FE(51.5=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