DreINT0007198 @ danRer10
Intron Retention
Gene
ENSDARG00000091398 | COL13A1
Description
collagen, type XIII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2190]
Coordinates
chr13:7735642-7737966:+
Coord C1 exon
chr13:7735642-7735686
Coord A exon
chr13:7735687-7737915
Coord C2 exon
chr13:7737916-7737966
Length
2229 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
CCTTTTCTGTTTTTCCTAAGGTC
3' ss Score
10.81
Exon sequences
Seq C1 exon
GGTCAGAAGGGTGAACCTGGGGAGAAAGGAGATAAAGCAGAGCTG
Seq A exon
GTATGTTCCACACTTCAATATCAATACACTTCAATACACACACAAACAAACACATATATAGTATATATATGAGCAGTATCACACAAGTAGTAGTGCGATATGGCTGAATATCGGCACTGGTAGGAGGTGTGCGTTGGAACGAGGCCGCAAGCCATTTGTTTTAGTGTCTCCACAGTAATGATATACAGCCATATCGCACTGCTACGAGTGTGATATTGCGTTTATACAACAGTTTGACCGCATAATCATCTATGTAAAAAAGAAAATTAAACAGGAGTCTAAAAACCCTTTTGTACAAGGAACTACTTTCTTCCGCCATTCCTTCACATCTGCAGCTGATGTCAGAAAAGCAGAAACCGTTGCTACTTTACCAACATCATAGAGCTAGTATTTGAATGATTCTCTAGCGTAATGTCTAAAGTGATGACAAAACTGCAGATTTTTCTCACATCCGTCTACAGAGATATCTTCTTAGAGTCTATTACAGTCTACAGTATTTCTCAGTTGTAGTCGGTATATTGTGACGGGTGCCAGGTGTCCCACCGTTTACCCAGAGACTTTTAGGAATGAAAAAAGTAGACAAACTATTTTTCTCTTCCTATTGGACTTTATGCATTTCTCATGCATTTTGTGTGCTGTCGACTACATACAAATATGTCACAAAATAAAATGTTACGTTATTAAAATAAAAGTATAATACAGCGGAAGAGCGACCATCACACACTTTTCTTTAGAGCAAGCTGAACTGAGCTCCCATGCATGCGTGCTTACATCTCAAAGGTAAAACGACCACAGAAGAAGTCCTCTTAAAGGGGACATGACATTTATATACAATGCATATCAAACATTAAGCGACCGTTACAATATCACAATAATTAACCCCGAAAAAAAAAGCAGCGCAATAACTACAAGACTCCTGTTGTGTTTGCGAGAAGGAAAAACACTAAACAGATGCGGGCATTTCATCTTTATTTCTGCCAACACAACACACACAACACCTGATGTGCGAGTCCCATATCTTACACTCAATGCGTTACAATTACTTAAGGTAACATTATAAAAACTGCAATGCAATATGCAAAAGAGAGAGATCGACTTGGAATATCACTTACCAGTTTAATAATAATTTGACCTACTGAAGTTACGCTGTTTTAATCTTCTAAGGGCTTATTATCTAAGTCTTTTTAAGGTGTATTCTATTATGCAGTCCTTTCACCATTTTGTGGATGAAAACGTTAACCATCTTTGGTCTACTACTCAGTATGGCAGGCTATGGCTGCCGTCGAGTTGTCTCTCAGAAATTGTAAATATTTTAAAATGGGCAATACTCTTAAAAAATAAGCTGCATAGTTGCAATTTAAACAACTATATTCTCGACTAAAAAAGCCTCAAAAGCACATTATGTTGTCCAACAACAGTAATATTTGTCAAACTGTAGACCGTCTTCTGCTTGTTGCTGACTGTATGTGGGCACGGGTGCTGATATTACTTAAATATCTAACCACTATCAGCCAATCAGATTCGAGAACCAGACAGAACTTTTGTGTGTGTGTATATATATATATATATATATATATATATATATATATATATATATATATGTATGTAATCACGGGGACTGACACATACAACTGGGGTAAGATCCAAAAGCAGGTTTATTCTTCGTCAGGCAAGCAATGGTCAATACAGGTGCAAACGGGTATGTGTAGGCAGTCCATAATCGTAATCAGGAACAGGCGAGAGGTCAAAAGGCAGGCGGCAGACAAAGACAAAGATGCTAACAAGGCTAAGGTCGGTAAACAGGATAACAAGACTGGGAAACTTGTTGTAGTGCTACTGACAGTAAACAAGACTCACTGAATGGGTGAGTGTGTGGCTTAAATAGTGCTTGCAATCAGTCTCTTCCAGGTGGTGCAAGTAATCAGTCTAGATGAGGAAGCAAGGGTGAGTGTGACTGGAGTGCATGTATTAATATGTAGTCCAGAAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAGACAGAGAGAGAGATATATATATATATATGTGTGTGTCTCTCTCTATATATATATATATATATATATATATATATATATATATATATAATTTACCTAAGTTGGTCATTAATAGACATTCCCTTTTCTGTTTTTCCTAAG
Seq C2 exon
GTCTATGGGCCTGCTGGACCTCCAGGACCTGCTGGGCCAGTTGGGCCAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000091398:ENSDART00000040379:28
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=FE(16.7=100),PF0139113=Collagen=FE(22.6=100),PF0139113=Collagen=PU(3.4=13.3)
A:
NA
C2:
PF0139113=Collagen=FE(29.6=100),PF0139113=Collagen=PU(19.7=88.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
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]