HsaINT1008142 @ hg38
Intron Retention
Gene
ENSG00000188517 | COL25A1
Description
collagen type XXV alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:18603]
Coordinates
chr4:108819252-108824227:-
Coord C1 exon
chr4:108824174-108824227
Coord A exon
chr4:108819330-108824173
Coord C2 exon
chr4:108819252-108819329
Length
4844 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACC
5' ss Score
6.78
3' ss Seq
GAGTTAATCTTTACAAACAGGGA
3' ss Score
5.95
Exon sequences
Seq C1 exon
GGCTTCCCTGGTCCACGGGGTGAGAAGGGTGATCTAGGAGAAAAGGGAGAAAAG
Seq A exon
GTGACCTCTCCATCCCAGCATGTACCTTGTTTGATTCTTCTCCTGCTGTCTGCTTTGCTGTTCAGCTTGTGTGATTCCATTTGACACTTAATCTTTCTCCATCCTGTGCTCCAAAAACATACTGATGCCTGATTTAAGGAATCAGGTCTTCAGAGAGGAATGAAGAAGGCTGTACTGCCAGATATAAGGGCACTGCCTGGCATAGAAGAAAAAATTATTATCACCAGATATTCTAGCTACAGTTTTTCAACCACCTGACACCAATTTATGGAAAAATAAAGGATTTTTGAAAAAAAAATCATTTTAAAAAGTAAAATTAAATGACACAAATCTGCAGTAGTATTTGGCAGAGCTCATTGAACCCTGCAAAGGCAGCATCTCACTTGTCTTCACTACTTCCCAGTAGAGAAATGGAGATATGTTTTGTACGTTGATATTTTTTATATGAAAATGGAGGAGAAGCAGTGTGACTGATAAACTACAGTAAGTTCACTACACAGGACTAGGACTTGCCACTTTCAGATTCAGAGCAACAGAGATTTTTAAAACAGAGATATTGGTGTATTTTATGAGGTTGATGTTGAAGTTCTATCTCAGAACCATCAGCTCCATGGTCTTTAGGAGCCCATGTCAGGCAATATGGTTTTATGACTTGAAAGAAAAGTTTGGATTATGGATTTTAAAAGTCAATTTTTCCTTTCCTCTCCTTTGTTCTTTTCTCCTCCTTTCCCTTCTTTACTCTCCTCTGTTTCTTTTCTCTCCTTCCCTCCCTCCCTCCATCCTTCTCTATCTCTGTCTTCCCCTACCACCCCTTTCTCAGTATTTTGCTTGGGTCTTTTACCTGGTAGTAAATCTAAGGAGAATTGTTTACACTGGACACAACAAAAGAAGCCATCAAAAACTCAATCCCTCAATAGAACAGTGGAAATCTTAAAGTGGCTGAAACTACATTTCACAGTACAAATTTAAACCTTATATTTCTCAGGTTAATTTATGTCCCTGCTCTATTTAACCTTATGAATTCTCTTGAACAGTGACATTCATAGCTGTTGACAAGCAAGGCTAAATGAGAGTTGTGAAAGAAAGAAGATTATTAAGCTTGTGGTGTAAGTTTTAGGCCTTAAGCATTGCTTAGACTCTCCTCCCACCCATTGGTAAGAGAGCCCGTGTAAGTGGTTATCTGAAAGCCCCATCATCATCACCAGTATCATCACATTTACTGAGCATTATGTGCTTTCCCAAGAGCTATACATATGATAAGTCTTTTAATCCTCATAACAACCCCCGAAGTTGGCATTATTTTCCCCACTTCACAAACAAGGAAACTGAAGTATAAAAAATTCTTTTATTCTGAATTATAAATTCTGACTATAAAATACATACGTTTTGAGATAAATTGTGCATATAAGCTTTTAGCCCAAGATGAGTGTGTTTTAAAGATGATATGTAGCTGGGTGCAGTGGTTCATGCCTATAATCCCAGTGCTTTGAGAGTCCAAGGTGGGAGGACTGCTTAAGGCCCAGAGTTCAACACTAGTCTGGGCAACCCATCTCTAGTGAGACCCCCATCTCTACTAAAAAATAAAAAAATATGGTGGGGCATGGTGGCATGTACCTGTAGTCCCAGCTACTCCAGAGGCTGAGGTGGGAAGATCACTTGAACTCAAGAGTTTGAGGCTGCAGTGAGCTATGCTCATACCACTGTACTTTAGCCTGGGTGACAGAACAAGACTCTATCTCTAAAAAAACTCAAAAACATATATATATGCATTTTATATTTACCTAGTTGGTTGTATGAGTCTAAAATCTTAATCACTCAAAAACATATTACCGCCGGGCGTGGTGGCTCACGCCTGTAATCCCAACACTTTGGGAGGCCGAGGCGGGTGGATCACTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGACGAAACCCCATCTCTACTAAAAATACAAAAATTAGCTGGGGGTGGTGGTGGGTACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGCCGAGATCACGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAGACCCTGTCCCAAAAAAAAAAAAAAAAATTACCATTAGGAGGATACTCACGTTTATGAGAAAGAAATTACCAGCATTACAGCATAGGAAAGCATAAAAGCTAGAAACTTGATCCTCAGAATAATGTTAATCACCCATACAAAATATTTCCATGTTCAGCTTCCATGATTAGAAGTTTTAAATTTACAAAAATTGGTTCTAAATGCGAATAATTCATGTATATAATTCTTTGACATGGGAAATAAAAGTTATCAAGAGCTCTCATGTACTCATACCCACAATGACATGGTTTTGTATTGCATGGGGAATCAGTGCATATTACAAAACAATGCTGACTAATAATAACATTGGCACGTTATTCTTCATACTGTAGTGTTTCTTTCCCATAAAGCTTGAGGCTCACTAAAATATTACTGAAAAATGATTCCTATAGCCTGGCACAGTAACATTCATATGACATTTTTCTGTTGAGTGGTTAATCTGAGTTGATTTACCAATCAAATAATGAATTGAATTCCAAAGTGATAATACCCAAGACACCTGGTCTCAGACACACCTATGTGAAGAAGAGTCCACTGCCCTTTGGGAGGGAAGAGCTCACCCAAATGAGTTTACATCAGTTTTATGTCATGGTACTGAAGTGATTTGTTAAGGAAGAATGTTGATCCATCTTGAGTGAGTGACCAACTTACTCCTGAATGTTCTTCCCATCTTACTTCCTATCACAACTGCTCTCATTTCACCCTGACTTCTGGGGTCATCATTGTCTTTGATCATGATCAACTAAGCCACAGAGAATGTCTCTTTGCCCCATATTCAAGAAATCCAAGTGTTTTTGATTCTGAGCCTTCTGATGCAATCTTTTTGGCACACAGGAGATAAATGAAGAGCTTTTGCTCATGCTGTCAGAATGAATGTATTGATTTGAATGCACATCTCATATATTTCTGTTATGTATATCTCTTTTAACCTTTCAATATTCATGTTGCTTTGCTTCAGACATTATTCAGTTTTATTGTAACTCCCATCCTGATTGCAGAATGAATACATTTATTTAAGTATGTATTGTATAGTATTTTGAGTTCTGCACGGCACTAACTCCCTGTCTATAAATATGCAGAGATACTGATGTTAATATAAAACAGCTGAGGTGCATTCCTTCCTACTCCTCCTTTTGCCTCCTTTCCTTAATTCCTCTGGCCTTATGATCCATGCAGATTTCCCACAACCTTTACCTTGATTCCTAAATACTAATTTCCATAGCTACATTCCCACTATGTAATTATCCTGCCTACCTCATTTTTACTGAGTCCAAGCTGCTTTTCCTCTCCTGAACAGATTTTTTTTTTTTTTGGCTTTTGTTACATTGTGAGTAAGCTGGAAACTCATTTACCATTGTAAATACATGGCATGAGATCAGTAAGAGAGTGAATTAAAGAAGATCCCTAGGTTTATAAATAAGTCTGTTTCTCCAGTTGGCATTGCTGCAAAGTATTAGCACTTTTAACATTTGTTTACCTGACTTAATAAGGAAAGTATTTGCTTTTAGTTTCTTTTAAAAAAAGTTTTGCTGTAACAAAAGGATGTAAAAAATATTAAAAGATATAGAAGCATATTTTAAGATATTGAATATTTTTGAATGAGAGTTACACAAGTAATATCAATCATAAAGTTGGATACATTTCAAAGAAATAGACACTGTTCATATTCTTTCCTTTTCCTCTGGTTCAATGCAGCTTTCATCTGTTACAGGATTAGAAAAAAGCAAGGTGACAGGTATTGAAAATTGAGTGAAGTATCCATTATTTCCCTGAACTTCATCTGCCACTGGCTGGCTTCAATGGTTTTGGTACCTGTCATCCTCACAGGATCTGTGACTCAGACACCTAATTCATGATCGTGACATTGTGGTCTAAGTTAGCACTTCTGATGTATCAGCTTTTAAGCCTCCTTCTTCTGTCTTGTTGAGTATCTTAAATAAAATCCCACATGCCCCTGCCCAGAATCCATTGTCACTCTGAAAATATGTTAGCTGTTATAATATCATGCCTTACCTAAATCAGAAAACAGTGGTAAATGCCCTTCCAGAATTTTCTTACCTAAACCATCTTTTGAATTACCGTTATTTTCCCCCAAATAAAATTTGTCTTTTATTTAAACCCTTGTATCCACAGGGGGAAAAGGGAAAGAAAGGCAAAAAGGGGCCTAAAGGGGAGAAAGGAGAACAGGGTGCTCCTGGATTAGATGCACCCTGCCCGTTGGTATGTCTGACTTGTGGAACTGTCTCCAGATGTTTGTGTGAGGGGATCAGATGGGAGAAGAGCAAGCCGGAGGGATCCGTAACAGGAGGGTTTCTGATTGGGCTCATTTAACATGGACTTCAAGATACCCAGAAACATTTATCAGTTATCCTGATACGTTCCACATCTCGTCTTGGGCCACTAGCTCTGCCTGGTTTCTTAACCCCCAAATATCACGGCACAATTGGAACCTGAATGTAAGATCCGAAAGGAACTGGCACGATTCCATACCCTTCAAAAGAGGAGGCCACTGTTTTCAGACAAGCCCCTGTTGTAGGAATATGTCTCCCTCCATTTTACTTTGCCCAACTTCACTGGATGTTACTTTTCCCTTCAGAGTTGCTCCTCTCCCAGCCTTTGTTGTTGTAGTTACTTCTTTCGCAGAATTTGTGCTTAAGTGATTTCTTGTGTTAGTAACATTATGAGTTAATCTTTACAAACAG
Seq C2 exon
GGATTCCGTGGCGTTAAGGGGGAAAAAGGGGAGCCAGGCCAGCCTGGCCTGGATGGGCTGGATGCCCCTTGCCAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517:ENST00000399132:35
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.873 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(15.5=72.2),PF0139113=Collagen=FE(23.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(33.8=100)
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]
SPECIAL DATASETS
- Autistic and control brains