HsaINT0038715 @ hg19
Intron Retention
Gene
ENSG00000188517 | COL25A1
Description
collagen, type XXV, alpha 1 [Source:HGNC Symbol;Acc:18603]
Coordinates
chr4:109738553-109740485:-
Coord C1 exon
chr4:109740408-109740485
Coord A exon
chr4:109738592-109740407
Coord C2 exon
chr4:109738553-109738591
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-COL25A1:NM_198721:35
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
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
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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)