HsaINT1008143 @ hg38
Intron Retention
Gene
ENSG00000188517 | COL25A1
Description
collagen type XXV alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:18603]
Coordinates
chr4:108817397-108819329:-
Coord C1 exon
chr4:108819252-108819329
Coord A exon
chr4:108817436-108819251
Coord C2 exon
chr4:108817397-108817435
Length
1816 bp
Sequences
Splice sites
5' ss Seq
TTGGTACAG
5' ss Score
0.92
3' ss Seq
TTTTCTTCTCTTTAAAACAGGGG
3' ss Score
9.33
Exon sequences
Seq C1 exon
GGATTCCGTGGCGTTAAGGGGGAAAAAGGGGAGCCAGGCCAGCCTGGCCTGGATGGGCTGGATGCCCCTTGCCAATTG
Seq A exon
GTACAGTATTTCTCTTTCCTACCACCCTGCATGCAGTTCCTTTGTTTATCACATGTTCATCTCTATCAGTGTAAAGTGGTGCTTTCTGGGCAAGCTTTACATGATAAACACACTACATGCATGTGCATGAACAGGCTCCTTCTGCCACTGTGCAGAGTCAGAGAGCAAGCACGCGTTTCTATCAATGAATGCAAATTAATCTCCTGATGTTGTTCTCACAACTGACATGACCACCTTTTCTGTGTTCTTTGGGATATTAATTTTTTCAATAAATATTTAAAGATTACATTAAAATTATGTGAAAATATTTGATGCAAAGACACTGCTAGACCATAACTTTTGGTTTTCCACCTAAGTTTGACTTTTTTTCTTTTTCTCTAAAAAAAAAAAAAGGTATTTCTGCCTTTTTCGCTATATTTCAATCAGGCTATAAATAAGGCCCAACCTACGGAATTCAGCTTCTGTCGTCAAGTGTTAACCAATTCAAGAGAATGCTTTAAGAGACCACAAAGAAGAAGACCAAACTTCTCTGAGCTTCTAAAGATGATAAAAGTCTGCAGCCCCAACCTTCTTCTTTGCCACATAACCTTTTCAGTTTAATGGTCTCTCCTTTTGAAACTCACTTTCCTAAAGTAGACCAAACTCCCTTATCTCCATTGGCATGAACTCAAAATCCTCCTGATACTAAAATCTAAAATTCTGCTGGTTGAACCTTCTCCTTGTACCAATCTGGCATTACCAGTTTTTCCCAAATATTTATGAAGCTTTTTAAAAGTGTTCTTTTTTTACATTTAAAATGAAAGTATATTCATATTTTCTGAGGTATAAATAAAAATTTTTATGTTTGCGTTGATGGTTATATTGGTCTGCATGTTCTTATATTATTCTTCAGGTATAAGCATGATTCTTTAAAGATAAATTTATATTTCTCTTTAAGAGATTGTATTTATATTTTTAAAAATTAAGCAGTCAGTGATTATAGTTAGAAAATCTCAATATGAAGTTCCCAGTTCTTTGTTTGCTTGGTATTGATGATAAATCATATTTTATGATCATTTTGTTGGTGGAAAAGTAGAAGCATGCCTTCTTGATGTACCAACTCTTCCTGCGTTATTTGTGTCATTTGTATCTGAAGAATGCATACACTTTAAAATAAATTTTGCAACACTTAGGAACCTCTTATTTTATTCAGAATTTGTTAACTTTTGAATAATTTAAATAGAGAAATCGATAAATGCTGTAGATAATATTTTATCATAAAAATATAGATAGGCTGCCTGTCCTCTAATTCAATTGAGTATGTTCTACTGTATTTACTTTCAATATAGAAAAGTGAAAAATACTGGCATGTGAAGAGCTATAAACTTCAGATAGAAATGGTTTATCATTGATTATTCATCATTATCATGAATTCAGCCATAGTCTAATAGTGACCGGGAAGAGAAGTTATTTTGGTTTACGTAATAGAGATACCAGTGAGATGTGTTTTAATGGAATTAAGAGTATAGATTTATTATCTAAAAATATAGATATGAATAGAGCACTATGCTTTGTAAATTGCTTTTTCAAAATTAGGCATAACATTTTCTATACTTCATGTGTTTTCAAAATGTGTACTCACTCTGGAAAACATTTGAATTTTCTTTATTTTACCTAACACTGGGAAATATATCGGGAGTTGCTAATTAGTAAAAGATGCCCATGACCAAAGTCACTAATGGGTAGAAATTTATTTTTAAGCCTCTGAGCATGTGAATTATGAAGTTTAATCACTCTTATGGAACCTGAGGAATTCTTTTTCTTCTCTTTAAAACAG
Seq C2 exon
GGGCCAGATGGCTTACCCATGCCTGGCTGTTGGCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517:ENST00000399132:36
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(33.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(38.5=71.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
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
- Autistic and control brains