HsaINT0039218 @ hg19
Intron Retention
Gene
ENSG00000197565 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:2208]
Coordinates
chrX:107398837-107402978:-
Coord C1 exon
chrX:107402692-107402978
Coord A exon
chrX:107400491-107402691
Coord C2 exon
chrX:107398837-107400490
Length
2201 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
TAATCTCCTGTCTGTTTCAGCAC
3' ss Score
9.31
Exon sequences
Seq C1 exon
GCTTTGCTGGCTCCTGTCTGCCCCGCTTCAGCACCATGCCCTTCATCTACTGCAACATCAACGAGGTGTGCCACTATGCCAGGCGCAATGATAAATCTTACTGGCTCTCCACTACCGCCCCTATCCCCATGATGCCCGTCAGCCAGACCCAGATTCCCCAGTACATCAGCCGCTGCTCTGTGTGTGAGGCACCCTCGCAAGCCATTGCTGTGCACAGCCAGGACATCACCATCCCGCAGTGCCCCCTGGGCTGGCGCAGCCTCTGGATTGGGTACTCTTTCCTCATG
Seq A exon
GTAAGGTCCTGCACTGTCTCCTCCCCCAGTTGGAGGCAAAGGGCCCCTTGGACTGGTTCCCAGGCTCAAGGGACACCAGGTAGAAAGCATAGAGTTTGAAAAGAAGAGAAATGCTTGGACTGGGCTTGGCTAAAGAATGGAGAACCCAGTTCTGCATGAATGGCAGGTAGTTATGGGTGTAGCGGAAAGACAGCAGTTTGCACCCAGTGGTTCAGGGGCTAGAATATCTGTGAGTCATAGGTCAATGCCCCGCCGTCTCCATGCCCGCTTCAGTTATGCCACACCCAAGGGAAGAGCAAAACACACTAAGATCTGGGAGGACAGTGAGGGAGAGGCTGTCACCACTTGGGGCCAGGACACAGTTTCACTAATCAGTCCAGCCATGGCACTGTCCCCTCTTCTCTCCACCCTCCCAGATCCCTCTGGCCTCTGCTGTCTCCTCCCAAAAGGCTTTGATGAGTGCATGCTGTGTTTATATGTCCTTGCTGGTATTTTTGCTGCCTCTCCATTTCGGTGTGAAGGCAGCGGCCAGCCATGCTGTGTGTCTTGCTAAGAAAAAGAATATCTGCAGGCCCAAAGAGGCATCAAGTCCCTCACATAATATCCTGTGAATACCTGGGGATGTTTCTTCAAATAAAAGGTCAGGTTTAGGGTCAGGACATCCCCCAGAGAAAACCACTGTGGCACCCATTGAAGTACTCTGCCTTGCCAGAGCTTCTCTGTTGAATTGCCAAGGGTGAGATGGTGAGAGAGTGTCTTTAAAAATGACCAAAGCTGCAGGCTCCCCAACATTAGCGTACCTACCTGGGGAAAGGTACTTTTCCTTGTTATGCTGTGTCTTTGGACATTGGATAGTTTATCCCAGTGTAATACAGAATCACCTCACCTGTCCTTCTGTCCTGTCCACCACCCTGACCAGGAAATAAGAAGAGGCCCCTGAGCTTCCACAGGAAATGGTACAAATGCTGTGTACTAAATCTCATGTGCCCTGCTTATGGGAGGGCTCTTAGCCCTTATTCAGAATCTCTTTACTCTTCCTTTACACATTAATTCTAACATACTAGAATATTATTCCTGAAGATATGTAAGGGTGAGAAGTTGGACTGCCTAGCAAGGCATCTTGAAGCAATGAGACATACCTATTAAAAAGGAGAAAATAATTCAAAGGAGGCCCAAGGATTCTACGGGCCGTACCCCTTGGTGTGGGGCTCTTGCATAATCATCCCCCACAAAAACTGACATTCACAATGACAAGCCTGATTCATCTGCAAAGTTTAAAATAACCTAGTGTCTGCTACTTAGCAAAGCAGGAAAATGTGTTGTGCATCTTAGAAAGTTTTTGATTCTCAGGGTCAAAGTGAGGAAAATTTTGATGCTTCGGTTGTCAGGAAAGGTCACCTGAAAGGTCCCATGCAGACTCTCACTCTTGCAAAGTTCTGCAAAGTAAGGAGTCCCTGTGTGCCAACTTGGGCATTTGTCTCATTGGCCATTTGCTGACACGGTTGTGTATTAGGCCTCTTCCCTATCTCCTTGTGGTCCAGATGATAGCCCGGCTAAAGTGAAGAGAAACAGGCAGGAGTGTGGAGAGACAGGAGCTGCTGTCTATGTGAATAGTAACTGAAAACCACCAGCTCATGTGTAGCCCTGAAACTGAATACTGAGAGAGCCCTCTGAGGTGAGGGCCAGGGTATTTGGGCCAAATACAACAAATTAAGGAGAACTTCAGTAGGTTTTGGACTGTCCTTCTTTCCCTTCTTAGAGTACAATGCATGGTTGAGAGAGGGCTCTGAGAACCGCAGTCCAGAAGCCTATTGAATTTTCCTTCACTCAGCTTTTCTCAGATCCATTTGTCCGAGGAAATTTTGCAAGGGGGTACCTAACACACCTCTGAACCCAGTGGGACAGTAGCAGTTTGGGAATTGCTGCTTGACATGTAGTCATTGCCCACATAATGGGTTAGGAGGGCACTAGGGAGCTTGGAAGGGGGCACTCTTGGCCCTGAAAGCTGCTATGAGGGAGGACAAGCAGCCCCTGCCCCTAAAACACAGCTCTTGGTATGCTGGCTTGAACTGGGGGCTGAGACAAGGAACCAGGGCTTAGGAATGGAGCTCATGTGCCCCTGTAGCAGTGGAGCACCCATCCCCTCCCCACACCAACCCTTGGCAGGCACAGCTCATGCACTAATCTCCTGTCTGTTTCAG
Seq C2 exon
CACACTGCCGCTGGTGCCGAGGGTGGAGGCCAGTCCCTGGTCTCACCTGGCTCCTGCCTAGAGGACTTTCGGGCCACTCCTTTCATCGAATGCAGTGGTGCCCGAGGCACCTGCCACTACTTTGCAAACAAGTACAGTTTCTGGTTGACCACAGTGGAGGAGAGGCAGCAGTTTGGGGAGTTGCCTGTGTCTGAAACGCTGAAAGCTGGGCAGCTCCACACTCGAGTCAGTCGCTGCCAGGTGTGTATGAAAAGCCTGTAGGGTGGCACCTGCCACTCTGCCCCTTGCCCTCCCCTGCCCCTCACAACAGTCACCTCACAAACCTGAATGGTCTGAAGAAGGAAGGCCTGAGCCCCTTTGCCTGTCAAGTTGTACATTGGAGTCTCATTTGGGCTAGACTACCGGACACTCGTCACCCCAGCCCTCGGGTCCATAGAGATGAGCCCACCCTGCTGAGATCTGCTGTCCTGTTTCTGTCAAGCTGGTGCTACTGTTTGATTTGGATGATTGTGTGACTATTCATGGCTACCTCAGAAAGATTTGATGGGCCACAACTGTCTTAGACTGCTAGCTTTCTCCTTACCGTCTTGATCGGAAAGCTCTTCCTAATCGCTAATCAGTCATTTCTTCATGTACAGAGGTCAGCACACATTATTTGGCTTAAACCAGAACCCAGTGTTTCCACACTTAAATTCTCTAACCGAATATTCATGGATGGCTCAAGTCTGCACAGAGCAAGTCCTCACTCTTCAAGGAGGCCCACTGTGTCTAGGCAGGCAAGAGAATTGAAATGAGGTGCCACCCAGTAGCCCAGAGTGAGCTTTAGCTCTCTCTAGAATGAGCAAGACTGGGCCCCACATGGCTTAGAGAGGCTTGAAGGCCAGCAGCTGGGTTGGGGGTGGTGGTCATTAATGGCATATGGTCCTAGACAAACCATCTCCTCCTTGCCGGCTCCCCCTCCAGCCAGAGACAGAGGATGTGGCCTGGTTCAAAGTAAAGCAGAGGATGCAACAAATGTGGCCAAGCCTATCAAAGGAAATGAGAATGACAGCCTTTTTTCCTGGGCCAGAAGTAGAGGGGTGGGTGCGTAAGGATGTGTGAGTTTTGCTTTTGACTCCAGGAACAAAAAGGTAAATCCCACATCCCAGTTTCTCAGAAGTCCCTGTTTATTCCAAATGCCATCCAGATGTGTGCAATGTGGCAAACTGAAGCTGCACAGTGTTGGTTTCCTTGTATTCTGAGGATGTTAAAGACTTTGTTAAATGGTTATCCAATTGCTCTTTCACAGGTAGCCTATTAAACTATTTTAATATGTTTTTTTAAACCTCATAAAAATCTAGCACACTCTTCTCTTGAGCAGTTAGCAGACCTAAAGCAAGCCTGAATTGGCTATGCAGTACATTGTATTCTGTTTGGGGGAATTTGTTTTAGCCATTTTCTTTAATTACCAGTTTTCCAGAACACTCTTAGCTATGTTGACATGAGGCAGTTCCTTCCAGGTGATTCTGTTTCCTTAAGTATTATATAAACTGTGCCAATACAGACAAAGCATAATCAATATAATCTGAATTATTGTTATCTTTACCTCCTGAGTAATAAGCATGGTGTCAGTTTTGTACATAGCAAATAAAATAAATGAAATCTGAACATGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197565-COL4A6:NM_033641:44
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.9=31.2)
A:
NA
C2:
PF0141314=C4=PD(72.4=96.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
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
- 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)