DreINT0007196 @ danRer10
Intron Retention
Gene
ENSDARG00000091398 | COL13A1
Description
collagen, type XIII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2190]
Coordinates
chr13:7733949-7735483:+
Coord C1 exon
chr13:7733949-7734083
Coord A exon
chr13:7734084-7735390
Coord C2 exon
chr13:7735391-7735483
Length
1307 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
ATTTTTTCCTCATTCTGTAGGGT
3' ss Score
10.14
Exon sequences
Seq C1 exon
GGTCCAAGAGGAAAGCCGGGAGAACCTGGACCCATCGGCCCTCCTGGACCAGAGGGAGCACGAGGAGAAGGAGGAGTCATGGGTTTCCCTGGGCCAAAAGGAGACAAGGGAGACATGGGCCCCTCAGGATCGCCT
Seq A exon
GTGAGTGACTGTACCAGCTTTTGCCATTATAAATAACCTGTCTGACCACATTTGAGGGTGCTTTCACACCTGTGTATCGATTCAGTTGTTCCGAAACAGGGATTAAAATTGTTACATTGTTGTAAGTACTACCACACTGCAAAGTTTCTAAACGGACCAAAAGAGCTAAAACAAGTCCCGTGCGAGTAAACTCTCCTCACATTGGTCAGCATGTCAGGGTTTATTTTGCAGAGTCCCGCTCAGCTGTCAGAAGAGTTGGTGGTTTGGTGGTGTTTGACAAAGTGCGTGCGACGTGTCTGAATAGCGAGGAGAGATGCGGTGGGGAGGGGGTGAGAAGGGTGCACGACGAATTTGAGGACCAGGGGGGAGACGCGTGATTACCGAGAGATTATCACTCATTTTCAGGCAACCAGAAGACTCCCGAAACTTCCCGCCCTACTCATAATTCTCTCTTCATATAGCCGTATGCCTATTACATATCCATAAAACACTGTGATATTACCGCGCTCGGATTGTATCGCTTTCTCACTGCAATCGATCCGCTCCAGAGTTCGTTTCAGTCGAGCCGAGACCACCTCATTCAGGCGATCCCGAGACGATTGATTTGCCACGGATCCTAGCACGATTGCTGGTTTCACATATGCCAAATGAACTGCGCTAACTGAGCAAACAAGACAGGTTCCGAAACAAAAGTGTAGGTGTGAAAGCACCCTGAGTTTGTTTTCTTTATCCCTATGATTAAATAACACTAATATTAATCGAAATATCATAATATTCATATATTCATCATAATAACCACATTGCCATAACCAAGTTATTGTAAAATAACTGGAAATTGTAGTAAAATAGATGATTTTTGCATGTATTAAAGAGGTGTGGATTCATTTAAACTGAATTGTCCACTGGATAAAACAAGAATGCATCTCCAGTACTTCCAGAGCTCAGTGTATTTGTTTGTTTGTGATATTCTGATTACAAGAACTTTGGAATTTTCCAATAACCTTAGAGTATGTAAACACCCTTATCAGATTAAACCAGAATGTCGACCGTAATGATTTGCATGTAAATATTTGAATGAGTGGAATCATTTTGAGTGCCTTGATGAATTTCTTTTAAGTTTGTTGTGGGTGGGCAGCACTGCGTTTATGAAAGCCTACTAATTGTTAATCCTCCATGTTGGATGCTATGACTTCAAATGTCTCCTGACCGTGGAGCTTGCTTTCAAGTGATGTTCACCAATCCACTTCTCCAATTGACTTTTCTGTCTATTGTATTTTCTATTTCCCCATTTTTTCCTCATTCTGTAG
Seq C2 exon
GGTTTAGATGGCCCTACTGGAGAAAAGGGGGTTTCAGGGCCCCCTGGCCATATTGGATTGCCAGGCCCAATGGTACGCAATGGTGGTCCTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000091398:ENSDART00000040379:26
Average complexity
IR
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(37.1=51.1),PF0139113=Collagen=PU(54.7=77.8)
A:
NA
C2:
PF0139113=Collagen=PD(42.2=87.1),PF0139113=Collagen=PU(15.8=29.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGAGGAAAGCCGGGAGAAC
R:
TTGAGGACCACCATTGCGTAC
Band lengths:
224-1531
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]