MmuINT0040050 @ mm9
Intron Retention
Gene
ENSMUSG00000067158 | Col4a4
Description
collagen, type IV, alpha 4 [Source:MGI Symbol;Acc:MGI:104687]
Coordinates
chr1:82515504-82520530:-
Coord C1 exon
chr1:82520426-82520530
Coord A exon
chr1:82515669-82520425
Coord C2 exon
chr1:82515504-82515668
Length
4757 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
ACCCTTAATTTTCCTTGTAGGCA
3' ss Score
9.53
Exon sequences
Seq C1 exon
GTGTTCCAGGGGACCCAGGACCCCCTGGCTACTATGGGGAGATTGGAGATGTTGGATTACCAGGTCCTCCAGGGCCCCCAGGCAGACCAGGGGAAACTTGTCCAG
Seq A exon
GTATGAATGTACCATGTGTTACAGTGAATATGCTGCATTGTACCTATGCATACCCATTGCATGAAATATATAGATATATAAAAAAAGCAACCCACGCTAGGACCGGCGAGGCACTGGCAGACAGGCCGACCTGTTCTCAGCCTGGCAGACTCTCTGACTCAGCTCCGAAATCGCTCTCTCTACCCAGCTCACTTAGCTCCCATGGTTGGCTGTTGCCATGCCCTCCCCATGCTTCCGAATTCTCAAGGCTGGCTGGGTGTACTCTTGCACACCTATGCTTCTTTCTCTCTGGAACCCAGTTGAGTTGCTGTGTGAATGAAAACACTACACAATCTTAGTTTAGAATCAACAGGTAACACAGTCGCTGGATGCAGAACCTAGCATCATAAGTTTTATGTTAGAAATTCTCCAGTGTCGGATCCTAATGGATCCACCACTGGAATGGACGGCCTCCGGCTACCTACATTGTGCATCCATGCTCTCTGCAGTCCAAAAGCGAGGCTCCTTTCTCCTGCCTCCTCTCCTCGATCCAGAAGTCCTCCTCTTGCCCAGTGATTGGTCCCTTATAATCTTTATTCATTAGGGGAAAATTCTACCACACATACCAGCTGAAATCCTCAATTCTAGCAAATCAGGAAGTGTCCTTAAGAGTGTTTAGGAAAGACAGATACCTGTGTCCTCTCCAGGACCCCAGCACTAAGCTCTACTGTCACAGCAACAGCCCTGGATTTCTAATGTGTTCAAATTCAAACCAACCAAGGGGAGGGATATAAGCTCATTTTTACACAGGTATGCACACACACACACACACACACACACACACACACACACACACACACACACACACACACAGAGGCACATACTCATACTATCTTGATCAATCAGAACTGTCATAAAGCAAGCATTTGTGTGACAGACTTTCTATCAGATTTGCACTTGCAGAAAAGATCTGAAACTTTTTGCTAGGACTGAAGTATCAGTTGTACTTAGTTGTTCTGGAAGATTCTCTCAGTTGATATCTATTTGCAAAATTCCATCTATGTACCCAGGTTCTAATATTCTATGTGAGATGTATAAATAAACACAATGATTTAAAAAAAAAAACCTTTCATACAGCCTTACTTAATGTGAAAGGCTCTTCCTCCTCCACCCATAGAAAAGGGAAATCAAGGAAAGCCAAGGTTATTTGACAGAAGCCTAGGGAAGCATTTTGTGGCCATTAGGACCAAGGACCCCTTTGGGAGCTGTGCCGGTCAATATTCCAGTGAGATCAGGAATAGGGGGGTTGGAACCTTTTTCTATTTTGTGAACCCAGAAGACCAGACTTGAGTAAACGTTTTGCCCAGCCCGTGTCTCTTGTATTAATCTGCGAAGTGAAAAAGTTTGGTAAGCTACACAACCACTAGCTACCAAATTCATGTTCACTGCTCCACAAAACTAGCTTCTTCCTTTTTTAGGGTCTGACAACAGCAATGCCAAAATTCCTGGTCAGGATCAGTCAGACAGAAGGAGGCTGCAGTCGGGAGTTTAAAAAAATCCAGGTTTATCTAAGCCAGGGAAAATATTCTCTTGGTCAGAAAACATTGAACTCCAGTCTTAGCTTTCTAGTTGGGGCTTGTTTATAATAAAATCATATCTTCAGTGGATTGAAATAACCCACTGGGAACAACATATTCAAACATACAGGGATGCTCTTAATTCCTTTTGAAAAAAATAAATTGATCCTGTGCTTGGAAGATGGCTCAGTCAGGAAATTGCTTCTCACACAAGCAAGAGGGCTGAGTTCAATTCCCCAGATCCTACTCAGGTGTGGAGGTGCACTCGTAGAATCCCAGGGCTGGTGACACAGAGACAGGCTGATCCCTGGGGCTCAGTGGCCAGACAACCTTGCCAAATTGGTGACTTCCAGGCCACTGAAGGACCCTGTCTCATAAAAGAAGATGGGCATATCCTGCAGCTGAGCTCTGGCCTCCATGTGCATACACACATACCTGCATATGGCTCCCCTCACTTGAGACACGAAGTAACACAATCCAGTAAACCCAAGGACTTTTAAATCTGAATATGGGCCATAGTAGACATTTTATTTTGCATTGTATTCATATTGCATTACATAAGTGTATATACATACCCACACTGGTTAAAATTCAGACTTTATAGGATAATTTTTGAGATATGACATACTCTATTTTCGTTTTTTCTTCTTTCTTTTTTGGGGGTGGTTTCAAGTCCAGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTTGAACTTAGAAATCCACCTGCCTCTGCCTCTCAAGTGCTGGGATTAAAGGCGTGCGCCACCACTGCCCGGCTCATACCCTATTTTCTATTCCATTCTTTTAACCTGAAAAAATAAACAAGTTAATACTAGCCCATTTACTTGATTCTGTTGGGTGGCCAAGCTAGATGTATACATTCTAGCCCAGTGCCTCTGTTGAACAGGGTTAGGTATTGCTCCTGGTATGGGACAAAGCAACAAATAGTACCTGGGCTATCCAGTGTCTGTGGTGAGTTCTGGCAGGTCAGGAAGGGTGGGAAGATAGATGATATCCAAGTCACAGAGACGTTTTCCTTTGCTGTCAGTATACCAGTGTATACAGATTGTTCTCTTTAATTACCCACTGTATCTTGCATGGGATAAGTGGGCTTCAGAGTCAGACACTCACAATTGAATCAAGACTTGTTACATAGTGTAGTGGAAGAAAGTGAACTATTTCCAGTCGATAGTCTTTACAAACTGTGTTGTCCTGGACATTTACTGTGCCTCTCTGTACCTCGGTTTTCCCATCTATAAGATGGGGTCCTGTTAGGATTGGAAGATGTGGTATGTGTAAAGGATTTGGGATCCAACCTGATGGGCAGTAAAGAATCAGTGTGTGAGCTCTCATTACGACTACTGACACTATCTGTGCCTGCTCTACCATTGCTGTACATAGTAGAGTGATCACTGCAATCCAGCAGACATTAGTTAAACACACAGTCATTGTGTGTGTGCCTAGAAGACTTTTAAAAATAAAAGATTTATCCTTCGTAAGTGATTAAGAGAGCAGATATTTTGTCTAATAGATGTTCCAATAGGTTTGTGTGGATTAATTTTATGAGTTTAGTAAAATGGAATGATTGGAGAATACAACAAGTGAAATATGTTGGTCCGAGTAAACCTAAAGAATGGGAGAAAGGTAAGAAAACATGATCCCTAGTTCTTGTGGGCTTGCACTTGCAACTTCTTTCAAAGGCAGCAATGCCTGTTGGTGTATGGGAGAGTCAAGTTTTAAAAGATTTTTATCGTTTATTTCTATGTGAGTGTGTGTGTGTGTGTGAGTGTGTGTGTGTGTATGTGTGTGTATGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAACTGATGCTCTCAGAGGCCAGAAGAGGGCATTGGCTCCCTGGATCTGGAGTTACAGGCTTTGGTGAGCTACTTGATGTGGGTGCTAGGAACTAAACTCTGGTCATTTGGAAGAGCATCAAGTGTTCTTAAACACTGAGCCATCTCTCCTGTCTCAAGTATTTTTGTTGTTGTTGTATCTGTATCAGTCTCTTTTTTTACTCTAATGCAATTTACTGGGATTATTCTGGCATGGCTCCTGCTTTCTAATTAGCAATCAGCCTTGTGAAAAAGCAGGGCTTTTGGTCTGTTTTTCCTTTGGCAATATACTCTATGTAGTCCAGGCTAGCCTCAATCAGTGATCCTTCTGCCTGCATTTCCCAAGCCGCTCCTCCTCTCTCTCACTCTGAAGCTTTGTTGACTAGCTGTTCACCTAAAATTGTGTCTGTATAAAGTATACAACTCGATGCCCTGCACATGGCCAGGTGATTACCAGAGTCTAGTAGATAAATGCACTGGCCATGCCTGCACCCTCACTATTGGTTTGTGTGCACGTGTACCTGCACGTGTATGGAAGGAGGATTTTACTTAAGATCTCCCTTCTTTGAAAGTGGGTGGGGGAAGAATTGTGGGAGAGGGTGACCAGGAGGTGGGCAGTGAGCCGGATGTCACATGAATAAGTAAAGAAAAAAAAAGCAAAAAACAAACAAAAAAACTTAAAATGAATGCAATAAAAATTCAAAAGATTAAAAAAAAAAGAAATTGAAGAATATAGTATAATGTGGAAAGATACCACGCTCGTGGATTGGAAGAATTAATATTGCCAAAATCTCCATACTTCCCTAAGAAATCTAAAAGATTAATATAAGTGTCATCAAATTGCCAATGAGATGTTTCTGTGAAGGAATGGACCTAGTAAACATAATGTTGAATATAGTAACCCAGACCCAGGAACTAAAAAAAAAAAAAAGGTCTCTCCTCTCAGTGATTTCCGGTACGCAATGTGGCTTGTTCACTACCGTCTGCTCTGCATGCTGTATAGAGGCTCTCCAGGATTTATTCAGCTCACCGGAAGTCCTGTCCCTTGGTTCATCACCTCTCTACTCCTTACTTCCTTCTTCCCCAACAACGGCCATTCTGCTCTCCTGTCTGAGTTTGATTGAGTTAGAGTCCACATGTAAGTGAGGTCACGGGGTGATTCTCTCTGTGTCTGGCTTGTTTTACGGTGTGATGCCCATTTCCAGACATTTTCCTCTAAATGTGCTGATTGTAACTTCTACCGAAACATATACTCTTGAGAACATGGGTAATTTCCACCCTTAATTTTCCTTGTAG
Seq C2 exon
GCATGATGGGACCTCCTGGACCACCAGGGGTTCCTGGTCCTCCAGGATTTCCAGGAGAAGCTGGGGTTCCTGGAAGACTCGACTGTGCCCCAGGAAAACCTGGGAAGCCAGGGCTACCCGGCCTGCCTGGCGCACCAGGACCAGAGGGGCCCCCTGGATCAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067158-Col4a4:NM_007735:19
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=FE(39.8=100),PF0139113=Collagen=PU(4.9=8.3)
A:
NA
C2:
PF0139113=Collagen=PD(29.5=46.4),PF0139113=Collagen=FE(90.2=100),PF0139113=Collagen=PU(31.0=48.2)
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
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: