HsaINT0038016 @ hg19
Intron Retention
Gene
ENSG00000197467 | COL13A1
Description
collagen, type XIII, alpha 1 [Source:HGNC Symbol;Acc:2190]
Coordinates
chr10:71655306-71657287:+
Coord C1 exon
chr10:71655306-71655332
Coord A exon
chr10:71655333-71657230
Coord C2 exon
chr10:71657231-71657287
Length
1898 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
3' ss Seq
TCCATCCCCTCCCAAACTAGGAG
3' ss Score
8.78
Exon sequences
Seq C1 exon
GGTCAGTGTGGAGAGTACCCACACCGG
Seq A exon
GTAAGTGAACCCCTAAAATTTAGCAGGGCACTTTGATCCATCCCTGGGGCACAGCGCCCAGCTCAGCCTCATCTCCCTGGGGTCTCCAGTTACTAACAGATCATGGGGGAGCAGGAGCACCCACTGCCCTCTGCACTCAGCAGTCAGAGAGGGGAGCTTGGGATGGTGGTGCGTCTGGTGGGAACAGCTGATGTGTCTCTCCAGCCATGTGCTATATGGAGCCGCTCATCACCCGTGCGTGTCTGTACATCCGCCCCTTTGTACGTACGTCTGACTCGGTATGTTGGAGTCTCCTGCTGTGTGTCTGGAGCTCTGTGGCTGCTCTGCACATGGCCCCCTGTGGCAGCGTGACTTGTGTGAGTCTGTTTGACTCCCCACCCAACAAGCATGTGTGTGCGTGTGTGTGGCGGTAGGGGGGTGGTGTCTGGCAGCCTAGCCGTGGCCAAAACAGTGGGACTTTTCTATTAGTCACTGTATCAGATGATGGTGTTTCACATCCAAACCTCGATGATGGGAGATAATCGGGGACTGACTGCAGCAATTCAAGGATAAAATCTCTCCTTGGCCTCTTTAAAAGCAGAGGAAACCCTTCTCCAAGCAGGGTGGGGATTTCAGGCTGAGATGGTTCCTCTGCCCACCCCCGCCTGCTCCTTCCTTTTCCTTGCTCCACCCCAAGACACAGAACCCAAAAGACTGCTGTTGTCCTGTTAGGAATCTTCAAACTTGTGTCCCAGCAGCAGGGTCGATCTTGGGACAGGGGAGAGCAAGATACGCACAGCTTCCTCCAGTAGGAGCCCCAGTGAGCTGGACCCAGAAAAAAATGCCCCTCATTTTGTGGATTGGCCTCGTTGCTCCCAGACCTGGACAGCAGGGATGGAAGATGAGCATCTTTAGGCATCTCTCCCCGCTGTCATGTGCCCCATGGTGCTCAGCTTCCCTGGCTGCCCACCCCTGCCAGGCAGGTCCGGGTGGTGCGATTTTGGGAGTGGAGACAGACATAAGCCAGGCTCAGTGCCAGCTTGACTCTAGAAGGCTGTCAGGAGGGCAATGCTAGCAGGGCCTAGCCTCTGCCCAGACCCTCAGGAAGCTGGAAGGCAGGCCTGAGGTCTGGGTTCCTGGGCCAGGGAACCACTGTGAGCCTGGTACGTGAGAGGCTGGGATGGGTTTAAGGCTACGGCGGTGCTGGGCCCGGGCTGAGGAAGGCAGGCCAGCAGCAGCACAGTCAGAGCCACAGCCTGTCAGCGGCATGTGCTCCAGGGATGCAGGGGCCCTGCTGTTCCGGCCAGCCTGATCCTGATACAATAATAGAAGGTCAGCTGTGTTTATTTGAAACGATGGGCTCACGGGGTTATTATGTTACCCGAAAGAAAGACAACATCCCCCAGCACAAAAGACAACACAACTGCAGACGCTTTGGTAGTGTGTCTCCCGTTCTTAGTAAGTGCTTGGGGTGGGGTGGGGGCAGGGCTCTCTGCCCCTCAGCCCAACATAAGGAAAGGGAAGAGCACAGTGACAGAAGGCTGCAGAATACCCCTGGCCACAGGGTGCAGTGAAGCCTGACCTCATGACAGTGGCACTCTGGGGAACATGTCAAGCGTGGGGTGGGGGCATAGATTTGGGATTCCAGCTGAGGGGCAGACCAAGTTTATTTAGAAGAGGGTAGAAAATCAGGGGCCTTCTAGAGATCTGTTGGCTTTCCAAGGGGTTGGGTTGGGGTGGCAGGTCTCGGGGCCTGGAAGACACCAAGAAATCCAGGTGGCCCCTCCTCCATTCCAGCCTGTGGCTTCCCCAGGGAGGGAGAGGAGAGGGGTGGGGAGCAGGGGAGCTGGTGTCTGTGGGCTCTCCCCTCACGGTCCCTGTCGCCCTGTCTCTGCCACCTCCATCCCCTCCCAAACTAG
Seq C2 exon
GAGTGCCTAAGCAGCATGCCAGCAGCTCTGCGCTCCAGCCAAATAATTGCCCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197467-COL13A1:NM_001130103:12
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.743
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(8.2=55.6)
A:
NA
C2:
PF0139113=Collagen=PU(1.6=5.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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]
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)