MmuINT0071335 @ mm10
Intron Retention
Gene
ENSMUSG00000091345 | Col6a5
Description
collagen, type VI, alpha 5 [Source:MGI Symbol;Acc:MGI:3648134]
Coordinates
chr9:105907126-105910699:-
Coord C1 exon
chr9:105910646-105910699
Coord A exon
chr9:105907162-105910645
Coord C2 exon
chr9:105907126-105907161
Length
3484 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
CTTTGCCTTCGGTGTTTCAGGGA
3' ss Score
10.53
Exon sequences
Seq C1 exon
GGGATAACTGGGCAGAAGGGGACACATGGCCGTCCTAGCTCCAAAGGAAGCAGG
Seq A exon
GTAAGTATGTCCCAGATATTTCTCTCCCTTATCACTTGTGATGGTCACAGAGACATAGTAGAGACAGCAGACCTGTGCCTGGAGAGTACATTTTCAGGCATTCTAAAATCTCAACTCCACTCACCGTTTGAGCCTGAGAGAATTCTTTCTTAGGAAGGACTGTCTTGCACCTTGTAAGATGCTTAGCAATACCCCCAAGCTCTCCTCATCTGCTTACCCCTTAGTAAACATCCAAAAATGTCTTTTCAGATACTGCCAAACATCTACAGCTGGTGGCTGTGGGAGGCAAAATCATCTGTGACTAAAAGACAGCATTCTTCAGGCTGCCTTTGCCTTTAACTTTCAAGGTGTTTCTGAATGCCTTTGAAGGGAGCCCATGACTTGAACATACACACTCTCCTAACTTAGCATCTGGGAGCTACGTCAGAACATTATGGGCTGGGTGGACACAATCTCAAGGTGTTTACACATTGACAGTGGAAAGGGAGCATAGGAGTGGCTTCTTCCCGAATGGACTCCCAAACCCTGGCTATTAGGACCAACACTGAAAGCCAACTCAGTGGAGGCCCTGGGGTAGCTTATAGCATCTTGTGATATCAATCCTACCTCCTCCCAAATAAGACATTAGATTTTTCTTCAATTTTTAAGGACTAACAAAGAAACCACATTACCTTCTATGGATTACTGAAGTGAGAGATGATAATTATTTTATGGGGTATGGCGGAAAGAAGAGTCCTTCTACCTACCCCTGGCTGGCTTGGAAGTCACTATGAATAGACCAGGCTGGCCTGGAACCCACCATGTAGATCAGGCTGGCCTCAAACTGACAGAAAATCTTCTGCCCCTGCCTCCTGTATGCTGGGATTATAGGTGTGCACAGAGATGACATTTGTGTTGAAAGCTCTTCTGTCTCGTACTCAGTATGGATGTGATAACAGAAAAGAATGTTCAGAGTCCTGGCTGGGTTTGGCCTTAATTTGTTTGGAGGGAATGAAAATCCTTGGCTTGCTTTTCTGAGTGTTGGATGGTTCTCATCCCTTGAAGTCAGCAGCCTGCTGCCCTTTTCCCTGGGAACAGAGGCTCCATCCTAGCCCATCTTGCCTTTGTTTATCCAGAATGGCAAAGATCCTAAGCCAGAGGGGCTGGGCTTCCCAAGCTTCTGGGACCATTCCCTAGGATTGTGTCTTCCAGACTCAAGTGGATTTAGATGTAATTGGGGGAGGACATCAGAGCCGTGAGATAAACTAAGTGTTATAAAGTTTAGAGATAAATATATCTGTTGGCTCAAGAGAAAAAAGGATTTTAGTTTGAAATAGGTTTATAGCTGACACATAAATCATGCACTTTAAAAACAGAGCTGCTAGGGAGCAGGGTAGGGAGTAATCCTTGGACCTGCTAACCAGTGCCTTTTAAATCACTGTAAGGACAGAAGGACCTTAGCCTTGTCCCTGTCTTTTACCTATTTCTCTGCTTTGTAATTTCTTTTCCTGCGAATTAAATAAAGCAACATTCATATTCATGTTCATAATCAAGCAACCCAGGGCTTTTCTGCCCTCTCCCCACGTTTCCAATGTAGGCCAGAGTGCTGTCGTGTGATTCAGAGCATCTTAAGTGGGTAACAACACACCCCAACCCAGGCATGGGCTCCCTGTGTGACTGAAGTTCAACTTACATGGAGTAATCATCACAAAGGCTGTTACTAAAACAATGGCTCAACACACTCACAGCCATACAGGAAGCCACATTCCAGACCCATGGCCTTTGGTGGATTTATAACATTTGTATGTCTAATGTGTCATCTGGTTTGTAGCAGATACTCATCTAATCACTTTCAAATACTCATCTAGTTGAAACCTGTAAGGCCCCCCTGCCAGGTGGATTATATCATCATATCCACATTAGAGATGAACAAATCTCAGAGACTTGGGCAACTTGCCATAGGTCACAATAGCTGGTAAGTGACTGAGCTGAGCTTCAAGCTCAGATGTTCTTACTTTAGAGTTTATGCTCCTAATGGCTGTGTGAGGCCTACTGTGCATTTTCTTTGGGCCACTTAGGCTTTAAATAGTGGGGCCAAAAGCAAGAGAGTGTGATTATTTCTAAGACTGCACCTCTAAGGAAAATGTTGTACAAAAACAACTATACATAATAAACATTATTCTTCCTTTCAACTTTTCTCCCCTCCCCCTCCCTCCTTTTTGTGAGGAAAGGTCTCTATTATCCTGTAGCTCAGGCTGGCATTGAAATGACTATGTAAACCAGGCTAGTCTTGAACTCAAGGTCTTCGTGCCTTGACCTGTCAAGTGATGTGATTATAGCCATGTACCACCATGACCAGTTTATTATCCTTGCTCTTATTTTTCACTTGTGTGTGCATGTGTGTGCACTTGCACCCAGGTGCCCATGGAGGCCGGAAGAGGAGGTTAAGTTACAGGTATTTGTGAGCCCCTTGGAGTGGGTCCTCTGCAAGAGCAGCAAACACATTTGCCTGGGAAGACCCTATGCTAGCCCTCATCCTTGCACTTTGATGGAGACAGAATGTGAAGTTACGCCAACAGTATCTACTTTCGACGGCTTTTCAATCTTCTCCATTTTCCTACTCCAAGAGCATTAACTAGTCATATCCAGAGACAGACAGCTGATGAGTTACTATGGTAACGTCTCCCCAAAGGCTATTTTAAAAATTTAATACTTGATGGAGATGATAGTTGGGTGATTTAACCTAAGGAACTATAGGAGAAAATGGCAGTTCTGAAATAATCCCTTCATAATAATTGAATAAAAGCAATTGCTTAAAATAATTGTGGTTGGTTATCACAATATAATATCAGTTGATGGTTGAGAGTGTTCCACGCCTTCTTCAGTGAGAGTAACGCCAGCAGAGTTTTATGGCTGAGGTTTGGGAAATATAAGTTAGGACTGGCGTCCAGGGCATAGTCCCTCCTGGCTTTCCTCTGTCCCAGAGCTTACACTTGACATGAACTGCTTCCCAGATAAGTGCAGACAGAGCTGAGGGACCAGCCTGGCTTTATTATGATAAACTTGGTCAGTAGCATCTAGAGCATACAAAGAAGCAGCCACACCCCAAGGGGTAACGGGGAGGGGGGGAGGGGAAGTGGGGGGCATGATGCACTGAGTGACTTACCTCAACGTCTAGAAATTTCACTTTTCCCTCTCCTCAGCACACAGTGCTTCATGGGTTTGCCGGGAAGAAAACAGTTCTTCAGGGTGATCTAGACCTCCAGATAGCCCATTCGATAACCATGAGAGATTATCAGACTGGGGCGGAGCTGTAGTGAATTTTACATTGGGTTACCATCAATCCCCTAAATGTTAATGTGATTAAAATGCCCAATGGAAAAGCATGCTCTGCTAAGGCTCCCAGAGAACTCTTTACGAGCAAGGAAGAGGAGAGACTGGTTTGCCTCAGGAACCGTCCTTCTGTCTGGGCACACTGACTGATGCTTTGCCTTCGGTGTTTCAG
Seq C2 exon
GGAATGGAGGGCCAGAGGGGGCCCCAGGGTCCCTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000091345:ENSMUST00000190193:20
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=PD(18.2=88.9),PF0139113=Collagen=FE(27.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
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
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types