HsaINT0038693 @ hg19
Intron Retention
Gene
ENSG00000188517 | COL25A1
Description
collagen, type XXV, alpha 1 [Source:HGNC Symbol;Acc:18603]
Coordinates
chr4:109784475-109790306:-
Coord C1 exon
chr4:109790244-109790306
Coord A exon
chr4:109784544-109790243
Coord C2 exon
chr4:109784475-109784543
Length
5700 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TGTTTTGCAATTTGTGACAGGGT
3' ss Score
6.45
Exon sequences
Seq C1 exon
GGAGAACCAGGTTTCATTGGTCCTCAAGGAGAACCAGGCTTACCAGGTTTACCAGGAACAAAA
Seq A exon
GTAAGTGGGCCTCTTTCTTTCCTTCTTTCTTTCTTTTTCTTTCTTTCTTTTCTTCCTTCCTTCTTTCCTTTCCTTTTCTTTCCTTTCTCTTTCTTTTATTGTCTTTCTTCCTTTCCTTTCTTTCCTTTTTCTTTCTTTCTTTTCTTTCTTTCCTTCCTTCTTTTCTTTCTCTTTCTTTCTTTTTCTCTTTCCTTCCATCTTTCTTCTTTCTCTCTCTCTCTTCCTTCCTTCTTTCCTTCCTATCTTCCTTCCTTCATTCCTTCCTTCCTTTCCTTCCTTCTTTCCTTCCTTCCTTTCCTTCCTTTCTTCCTTCCCTTCCCTTCCTTTTACTTTCTTCCTCCTTCCTTCCTTCCTCCCTTCCTTTCTTCCTTCCCTCCTTCCTTTCTTCCTTCCCTTCGCTTCCCTTCCCTTTCCTTCCCCTTCCTTTCCTTCTTTCCCTTCCCTTCCTTCCCTTTTCCCTTCTTTCTTTCTTTCTTTCTTTTTCTTTCTTTCTTCCTTCCTTCCTTCTTTCTCTCTCTCTTTCTCTTTCTTTCTTTCTTTTTTCTTTTCTTTCTTTCTTTTCTTCCTCTCTCTCTCCCTCCCTCCCTCCTTCCTTCCTTCTTGCTTGATTTCTTCTTTCTGAAATCTTTGTCATATATTTTTAGTCCACTATGTTGAAAGAAATGTGGGACAACTTGGTAATTTAGGTGACCATATATTTTTGCCTAATAGAGAATGAAAGCAGCTTAATCTACCCATTACTAACACTTCTAATGGCACCACTGTGTTCAATATTGAGTAGTGGAAAGTTAATCTAGAAAGCCTTAGGCAAGACAACAGGATGGTGAAATATTTCAGTTGTTCCACTTGTACCCCAAATTGCTCCTAAATTGATGGGATGCTATTAGCTTCCTGGCCATATGGAAAAGTAGAGAAATTCTGAGGAGGAGAGATAGAACTCATTAACTCCTGCTCCTCATCACCAATTTCAGGATATACTTGTAAATCAAAGGTTATTACTATTCCCATTACTCCCCAGATTTCAAAGGCAAGTACTGATGTCATATAGATTCCTAAGTGCCTCATCCCAAAAGGATCTACTCTGAATAACGTCTGCAAAAATATTCTATAATGAAAACCATCTCATGATCTTCTACTTGGCAAACCTAGGGAGGGCTCTAAAAGCAAAATCTATATATACTGCCATGCAAAAAAATATATATATATGCTGCTATGAATACAGTCAGACCCAGAGTTCTCTTTTTATCTACCCTGAAAGACATAAAAAGTACAGCTCTGATGATGGAACTTTACTCATGACAGACTCATGAATCAAAGAAGGGGCAAAATTACATCAAACTACATTCTTTTATTTTTAAACCATAGCAGGCTTTGCCTCAATGTGTACTGCATTCAACAGAAATAAGCCAGGGATGATTTCCAAGAGTTACAGAAATATGTTCATGGTCTGTTCTGACAGAAGGGCCCTCATTTCTGCTGGTCAAGTGAAAATAACTCTAAACCTAGTAAATGGAAACTATGTGTGTCCTAGGGGGGACTGAAACTCCATCAGATTATGCAAAATTGTTTTCTCAAGAAATTTCTTCACATAATGAGCTGTCAGGCTTATTAACAAAATATGAGGAATGCCTGTTTTAGCCTGAGCAGATTCACACAAGAAATGTCTTTCTGGAATAAAAAGAGAGAGTGAGAGCAAGAAAATAATGAGCATTCCCTGTTAATACAAGAACGGTTGCATTTATTCAGGCTTGCAGCCTCGGACCCAGGGCAGGAAAGAAGTCAGCCTCGCAGATGGGCATGATACACAAAGAAAGGGCGGCCTGGTCAATGAAGGAGAAAGCCAGGCGTGAACTGGATCTAAAAGTGTGTGTGGCATTTTGTGTGCTGTGCAAGGGAAAATAGAAAAAACACAAGCAGTAGAGAGTGAAGTTCATTCCTAAATATCTTTTCTTTAGTTTCCTGATTTTAAACTATTCTGCAGTTTCAGAAAAATTTCCAGATGTAGAGGCATAAAATCCACATTAATTACTGTTATGAAGAACCCAGCATGATTTTATAGACCAGGTACTCATATAACAGATACTACTCTGAACCCTGAGTAAAACTAAAGAATGTATTCTACCTATTTTGTATTTCCACAGAAGGGATATGGATAGGAAATTCATTTTACTAACATTACTTTGAGGTTAATTGTCAGCTGAATTACCTACCTTAACTCAGCTGTTAAAACAGCAACATGCATGTGCACACATATACACACATCATCGGTATTATTTGAAATATCTAATTTGTGTTGAATCCACATATGTTAAGTATCAATGTTATGGTTGGTTCAGTGTCATCATGGGAAAGTCATGGTTATTTTAAAAATCTCTTTCAGCTGAACACCATTCTTCCACTTGTGTAGACAGTCTGGATTTGTACCACTAAATTCAGATTTAAAAAGTAACTAAGACTATATTTCTTATTCCCAACACAGTGAGGAGAGATCATAATGAAGGAAGATGTACAATGGCATCAAAACATGCTGCATCTTTTATACCTACATTAGTGCCTGAGAGGGACCTCTATCAGGCTAAGGAAATAGGGGGAGGGGCCTGGGCATGGTGGCTTACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCAGGCAGATTGCTTGAGCCCAGGAGTTTGAGATCAGCCTGGGCAACATGATGAGACCCCATCTCCACTAAAAATACAAAAATCATCTGGGCATGGCGGCGCATGCCTGTAGTCCCAGCTACTTAGGAGGCTGAGGTGGAAGGATCACCTGAGCCCAGGAGGCAGAGGTTGCAGTGAGCCGAGATCACAACACTGCTCTCCAGCCTGGGTGACAGAGTGAGACCTCAAAAAAAAAAAAAAAAAGAAAGAAAAGAAATGGGACTATAGTCAGAATATTTTAGAATACTTTTACTAATACTGTTTATTCATTAATTCACCAATGTTTTGATCAAATATTTTTCTGCATTTAAGCATGGGAAGTAAATGCAACAGCAACAGTTTCTATTCTCCTGAAGCTTACATTGTAGTGTGGACAAGGAAGAGATGGAAGGAGGGAAAGAAGTAGACAAATAATATAATTTCAGAGAGTGATAGGGAACTAATAAGAGACATAATAAAAAGTGATTCTAGCTGAGTGTGGTGGTGCACACCTGTCATCCTACCTACTCAGGAGGCTGAGGCCAGAGGACTACTTGAGTCCAGGAGTTTGAGGCTATAGTGTGCTATGATAGTGCCTGTGAATAGCCACTGTACACCAGCCTAGGCAACATAGCAAGGTCCCCTCTCTAAAAATATATAAATGTTAAAAAGTAAAGATGTATTGACTTCACTCTTGTGGTGAACTACAGATAAATTATTTTTAAGGGTTTTTGTTTTTCATAGTGGACTGTTTTAGAATTCTGTAATTCTTAAAGTAAAACATTAAAAGAAACACCAAATACTTTACAGTTTTTTAATAATTTTTATATACCAATAGAAGCTCCTTAGTCTCACTCAACAGGGTAATGGGGTGGGGGATGACAAAAAGCAAAAACTCTTTTCATTTCTGGGCCATTGTGTCTATCTCCTGTATCTAGAGAAGTCCCTTGTCTTTCTCCCAACCTCTCCATTTTCACAACCTCTTCAGTGCTGTTAAGAAACCTGAGTCTTTAACACTTGCCTCCTGTCTTTCTTAACCCTTGACTAACCTATCCCACCTCCCCTATAAAACCACAAAGGCTTCCCAAAGTGGGCATGATACAGATAAGAATCTTGGAATTTCAAGCCCTACATGACCCACCATAGATCTAATTCTATTTTCTTATCTTTTCCAAGATGAAGTATTTCCTTCAGTGAGGAGAGCACCTCTTTCATCCATAAATATGTCATCAACAGTCTGAATTCTAAATGTTTGATGATTGAAATTCTACCCCTTATGCAAGAAGCCAGACACTCTTTACTCTGTGTTTAGGGAGTATTAAAAGGTACCATCTTCCTGGAGGGCAATTTAGCAAGTTTTTAAAAATATTCATACTTTTTTGACCTAGCAATTTTCCAACTAGGAATTTATCCTGAGAAAATGATCAACGATGTGCAAAAGATTTACATTTGAAACATTTATGCAAAAGTTGAAGATCGAGTACCATCAGTTTTACCCACTTTAAAAGCTTTGTCACTTTGAGCAAGTTACTTAACCTCTCCAAACTTTGGCTTCCTCATCTGTAGAATATGGATAATAAAACTTTTCTCATTTGTCCTGAGGATTAAATAGGATAATACATGTAAAGTGTTTTGTGCAGTTTCTGCACTCATCCATGCTACAGTCATTAACAGCAATAATTATGAAATAAACCCTACTCATCCTTCAGGACACGACTCAAGTCTCACCTCCAGGGATCCAATCCACAATAATAGATACCAACAGGGATTCCCCTTCTGTCACATAGGGCCTTACATTACTCCTTAATCCTTAACTATTTTGGTTCTGCAGCTCTTGTCTGCCTAACTAGATCACTAGCTCCTTGAGGACAGTAGCCATATTTATACTTCATAGAGATATGAATATATTAAAAAACTGTAAAACCCGAACACTTTTACATTCATAAACTATGAGATGAGTACTATAACTTTGTCCATTTTACTGAGGAAACTGAGATGTACAAAACCTAACTAACTTACCCTAGAACACAGAATTGGTAAATAGCAGAGCCAGGAGTAAAACCTAAGATGCTAGATTACAGAGCCAGGAACTTAACCACTTTGCCATGCTTCTTGCCAGCAGTGCTTAAAAAGTGACTGCAGAATGAAAATGGATATTCATTCCTATCTTGAGGTATAATGATGGCCTTTATCAATTCCCTTTAAAGGTCTTTCTATTTACCAACATAGCTATTTGACAGGCATTTACCAAACCATTTCCTTATCTGTAAAATGGAGATGATAATACAAACATTGGATAATTGCATATTAGTCAAGTTTCTCCAGAGAGACAGAACCAATAGGATATATATAGGGAGATAGATAGATGAGTGGGGATTTATGAGGGGAATTGGCTCATACAATTATAGAGGCTGAGAAGTCCCACAACAGGCTATCTGCAAGCTGGAGGAGACCCTGGGTTGACGGTAGCATGGCTCGGTCCAAGTCTGAAGGCCTCAGGTCCAGGGAGGCAGATGGTGTAACTTTCAGTCTGAGGCTGAAGGCATAAGAGCCTGAGGGGCACTGGTACAAGTCCCAAAATCCAAAGGCCAGAGAACCTGGAGTTCTGATGTCCAAGGACTGAGAGGAAGGGCTCTCAGCTGCGGAAGAGAGAGTTTGCTTTTCCTCTTCTATCTGGGCCCCCAGCAGATTTGATGGTGCCCCCTCACGTTGAAAGTAGATCTTCCGTACTCAGTCAACAGACTCACCTGCCAATCTCCTCCATTAACACCTTCACAGACAACCCAGAAGCAGTGCTTTATTATCTTTCTATGTGTCCCTTAATCCAGTCAAGTTGACACCTAAAATTAACCATCACAAATTGTTTTGATTATAAAATGAGATAATTCATGTTAAGAGATTAATAAAGTGCTGGGTACAGGGTAAATCAATGAAAACTCTCTGCTTTCTTTGGTTTCCTTCAACTCATTTATTAATCTACAGGGACCAGCCTGGGTGGGGGGAATGACCATTTACCTGTTTTGCAATTTGTGACAG
Seq C2 exon
GGTGAACGGGGGGAAGCAGGGCCTCCTGGAAGAGGTGAGCGAGGGGAACCTGGAGCCCCCGGACCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517-COL25A1:NM_032518:19
Average complexity
IR-S
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(17.2=47.8),PF0139113=Collagen=PU(22.8=56.5)
A:
NA
C2:
PF0139113=Collagen=PD(16.1=43.5),PF0139113=Collagen=PU(22.8=56.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)