HsaINT0038049 @ hg19
Intron Retention
Gene
ENSG00000197467 | COL13A1
Description
collagen, type XIII, alpha 1 [Source:HGNC Symbol;Acc:2190]
Coordinates
chr10:71712638-71716798:+
Coord C1 exon
chr10:71712638-71712724
Coord A exon
chr10:71712725-71716759
Coord C2 exon
chr10:71716760-71716798
Length
4035 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGT
5' ss Score
7.12
3' ss Seq
GCCTTCCTTTCTCCTTGCAGGGC
3' ss Score
13.52
Exon sequences
Seq C1 exon
GGGGAGAGGGGGAAGAAAGGCTCTAGAGGGCCTAAAGGGGATAAGGGAGACCAAGGAGCGCCTGGATTAGATGCCCCCTGCCCATTG
Seq A exon
GTATGTTTTTGTTTATCACTTGCATTGTTCTGGTTTTTGTTCTTGAGGTTTGTAAGTTGGAAACAAAGAAGGCAAATAAACTAAGATGAGAACCAAATGTCTACACGGATGCTACCAAAATCTCTCTGTTCATTTGACTGGTGAAATTCTGCCCGCTGTTGGATTTGCTTTGTAACCACAGCTGCAAGTAATTCTGGCTAAATCCCTTGCCTTTGAATCCTTTTCCTTTGAAGATACAGAGCAATCGATGTGTGGAAGTGAGGAAACCACTAGGAAAGGGATTTTCAGGGAAGGCCTCAGCTCTTAGCTCCAGGATGGCTTTGGAAGCCAGTGTAGCATTTGTGAGCCACGGATTTGCCTTCTTCGTTTCATGGCCACCTCTGTGGGCCAGTAGTTCAAGCTGTCTGAATCCTCACTTGATCAGGATGCAGGACACCAGAGTTAGCGTCTCCTCAGGGCCACTGATGCTCAAAACTGGGCAGAACAAGGCCAGATGAGGGGCTTCTAATGCACAGCCTCCCAACACTCACCAGCCATCCAGCTGAAACCTTTAAAGCTGCAGACCAGAACTGGTAGTCAGACAGACACCCCATGGGAAGCCTTCTCAAAAGAGCCAGCAATTAATGATGAGGCACTTCTGCTGGGTTTCTCAAGTGCCTTTGAATCCATTTGAAGGTTCTAAAAATTATGATGCACTAAAGTTGAAGTTTGTCTGTGTTTACACTAAGTGAGTCTGTAGAGAGAGGAGGATCAACGGAGAGGGGGCAGGTTGTATGTGTGCAAAGCTGAACTCTCCAGAGCACAAAGAGAGCACAAAAGCTGGATTTGGGAGATGGGGGATCACCTGGGATTTAGCCCCTGTTTGTAGATGCCTCAAGGGTCCTGCATCCTGGCCAGGGTAGGACTGGGCCTCTCTATTCCATGGTTGGAGCTGGCCAGCCTTGACCTGAATAATCATCGTGGTTGGTTTTGTGAACAGGGACACCGAGGTTTTAAAGGAGAGAAAGGGGAGCCGGGGTTACCAGGGCTGGACGGACTGGATGCCCCATGCCCATTGGTATGGCATTGCCCTTGCTTGCCTGCATGGCCGATTTGGGCTTCCCCATGTGTGTGATTCATACTGGGTTTCTCCCCAGCCACCCTCCACACTCCTCCTCCATCCCCCCCAGGCTCCACTTCCCACTTCTTCATTCTGTAAATGCCAAGGGTCACCCCGCCTAGGCTAGTACTCTGGGGGCTCCCAGTCATGCCACCCTCTTGCATGCAAAGTTTACTGGGATGTTTCCTGGCTTCCTGCTGCAGCTACCTCTAAAGCACAGCCACTTGATGCCAGCCAGCTCTCCCACCCTGAAGTTGGTTTTGGCTGCCTCTGATACTCATCTCCAAGCTGATTCTAGACAAAGCTGCCACCAGATACCAGCTAGGAAAGTGGATTCTCTGGACTGGTTTTCAGAACCATGACTCACTTCTTTTCCTTCAGGCAGTGAAGTTAGTTCAGAATCACTGGCTGAGCACCTAGCGAAACATGTGAATGAGATGCCTGATCAGCCCTGTATCCCCTGCTCCTCCATCACATGATTTGGGGGACAGAAGGGCATGATTACAGAGTAGACTGAGAAGCTCTAGAAGTGAGCTGGAGGAGGGGCCACCTGCCTATTCTTCCAGGTTGGATCGTGGGTCGCTGCCCAGGTGACACCATCAGAACTAGGGGATGGTCCAGGATTAGGTTTTCGGATCCTAAAGGGTTTGTCCTTCTTGCTTAAATCTCCAAAGACATTACCAGACCCTTCCTCGTCCCTTTCTTTCATGATCAGATGGCTTCTTACTGAAGAGTCTGGGAGAGACGGAAAGGTCAAGAATGTAGTTAAGGAGGAGGCAGGGAGACAGCTAAGGACCTCTCTTCCAAGCACGTCCCAGGCGAAGTGGTAGCAGTTTATTCCCGCCTGCCCAGTCCCTCTCTAGGCATGGACAGTCTAGGCCTCCACGCTGATCCTCTTACTGCAAAAGAAGCTGAAGGGAACACTTCACTCCAAGGCTCAAGGGGTTACAGCTCTCCCCAAATTTCCCCAATAGGTTTGGAGTTCAAGAGCTATTTTATCATACCAGTAATAAGAGAATTTGGGGTCTCACATCCCCGCCCTGGGGTCACACAGGAATTCTCTTTGAACAAAAGAGAAAAAGATACAAGAAATTATGCTGTGTGACCCTGAAAGGTGGTCGTAGAGCCCCTTGAAGGGCAGTAGGGACTTTTTAGGAGGAGCATAGGCAACAAAAGGAGAGTGCAGAGCAAGCAGGCGGGTAGCATGCTTCCTGTCCCTGCTGGTCCTGCCAAACCCTGCGCTTGCAGACTGCACAGCCACCTTTCTCAACCAGGACTTCCACCATCCACGCACCAATGGGAATGCCGCTCTGGCCCGCAGGGGCTCCCTTGAGCACTGGCCAGGTCTTCCCTCAGCCACAATCCCCTCCCACAATCTGGGCACCTTTAGTTCTGCCAGCAGCTGCCTTGGCCTCTCTGTTCCTCACCATACATTACTTTTCATTCTCTGCCTGCCCTGCCCTCCATATCCCCCTGCCACCATCCACACACCAATGGGAATGCCGCTCTGGCCCACAGAGGCTCCTCTCCCTCCCGGCATCCATGTGACGTGTGTCATACCGCACCGTGGCAGGCTGGGGAAGGGGCACAGGGTCACCCTGAAACTGTGGAATGCACCTCCTCCCCCTGCAATCCCCTCCCCAACCCAGAGGGGAAAATGAAGGTCACCCTGATTTGACTCTCCATGTAAAATGGCATTTTCTTCCATAACATCCCATATCAATGTGTCAATTTTCTATTAATTTTACTGGGGAAGTGTCTTCCCCTTGTTTCTCACTCTGCCTCCTCCTCTGTGTTATTATGGGCTTGAGGGGCAGGGGTAGCTATTGCTCATGACTTTTACTACAAGATAACCAGACTTCCTAAGCCCTCCATATTGGGACCAATTTCTGCTGAATGCCAGGTGATGAGAGGTTTCAGCCCCTGGCGTGGGTGGATGACGTCAGACCAGGGCAGCAGAGGACTCTCATTCCACAAGCTCCCTCAGGACTGAGCACTTGCTCCGGGTCTCCTGAAGCCCCATGTCCATCTCCTTGTCTGCCCTGCCAGTCTAGCAGACTTGGGCTGAGAACCAGACCTTTGCCCTTGGCCCAGCCTCGCCTTCCCCACTGGGTCTCTAGATTTCTAGATTCCCCATAGGGTATGCCAGCAAGGAGAGGATATGAGGGCCCAAGAAAACTCAGGAAAGTTTCTATCACCAAGGGCAGAACACGAACATCTTGAGGCTAAAGGAGCTGCATGGTTGCTACCAACAAAGGAGACCGACGGTGTGCAGTTGATTCCCATGTTTTTACTGCACTTCACCCCCAAATTCCCAGCAAGGTCTAAGGCTTCGCCAGGAACCCTTGTCTTCTTGCCAAAGGCATGTCAGGGCCATCCTGCAATACTCATGAGGTTGCCTGTCCCTTCATGCCCCTCACCCCACCCCAGGATTAATCATCAAAGAAGGACTGTCTACATGTCCTCCTCCCTGTGCTTAGGAAGAGAGACAAATAAGAGAATGAGAAGGCTGGGAAGGCCCTTAGCGGTCACATCAAGCAACTGTCCTTGCCAAGGTTTTATGGAGGAGGAAACTGAGGCCGCCTTGTGCTGAGTGGCTTACCCGTGAGCAGCCGGCACTCCATAGGGCCACAGCAGAGACTGTTTCTTCGTGGCACGGAAGGACATCTCTGCTTGCTGGTCCCACGGGCTAGGACAGCCCCTATTGACGTTGCACTATAGCTGCATGTGACCTTTAACCAATGGTAAAATAGCCGGATTTGTTTCCACCTCCTTCTGAGGTTCTGACCTGTAGTAGAGAAAAGAAATAGACAAGCGTGGGTGGGCCACATCCTGATCAGCTGCCAAAATGCGTGTGGCCCTTGTTACCCCTGTCCTGCCCACTTGGTGGACCATTGCAGGAAGTCTGAGCCCTCTGCCTTCCTTTCTCCTTGCAG
Seq C2 exon
GGCGAAGATGGCTTACCAGTCCAAGGCTGCTGGAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197467-COL13A1:NM_080800:36
Average complexity
IR-C
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(1.2=3.4),PF0139113=Collagen=FE(40.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.0=53.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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
- 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)