MmuINT0039541 @ mm10
Intron Retention
Gene
ENSMUSG00000079022 | Col22a1
Description
collagen, type XXII, alpha 1 [Source:MGI Symbol;Acc:MGI:1916950]
Coordinates
chr15:71795795-71801954:-
Coord C1 exon
chr15:71801877-71801954
Coord A exon
chr15:71799521-71801876
Coord C2 exon
chr15:71795795-71799520
Length
2356 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
TCTTTTGCTTCCTGGGCCAGGCC
3' ss Score
7.23
Exon sequences
Seq C1 exon
GTGAAAGAGGAGCCAAAGGTGACCCTGGCACACCTGGAGTTGGTCTCCGAGGAGAGATGGGTCCTCCTGGAATACCAG
Seq A exon
GTATGAAGGATCAGGGTCTCAGCCTGGGTGAACATCAACCATGGAGGCAGGGGCACACAGTGGTACCCTCGCTTGTGGGAAGAGAGGAGGACCTGGGCCACTCTAAGGAGAAAAAGAGAACTAGTTGTTTAATGGAATATTTCTCAAGTCCCATGAGGCATACCTTCTAAGTTGAAAGTCCCAATGACTTATTTACTATTCCAAAATGACCAGAATAAAGTACATTGATGATATAAAGGTATGATAAATATTTGGGACGATTCAGAAGCAAGTTTCTCCAATTTGTTCATTGCATATTGTACTCATATCCCCCTTAAAAAATCTCATTGTAGGGCGGAATATTTGGCTCAGAGATTAGGAGCACTATCCGCCTTTTGTAGAGCAACTGGTTTAATTCCCTGGCAGGTCACAAACTTCAGGGATTTAATATCTTTTTCTGGTATCCACCAATACTGCAAGTACATGGTGCATGTACATAAATGAAAGCAAAAGAGAATATACATGAAACATAACTAAATAAGTACTCATTAAATACACATCATGCCCCAGAAATATACAGAATTATTATGTTCCAATTAAAACTAATAAATGACTAAATATTGTGAGAAATCATCATGGGGAAAGAGAGATTGTTGTATTCTAAATGAGTCTGGGCATGTTGGAGATGCACCTCTCCTTAGGACTTTCCTTCTATACTTTAATTCATGGTAATTGGTTAGAACCCCACAGGCAGAGCGACAGCCATCTTCTTAAATCCCATACTAATTCATTAGTATTTCTCAGAATAGGCCCAGGGAGCCTTAGCCAAAGGTTTAGCTAAAGGCCAGCCCTCCTGGAGCTGAGAGGTGGCAGGGTCTTGGGACTTTTACTTCTGAAACTTAGAAATAACTAGGGAAATGGTAGCCAGTTGACCACTGTGCCTTGTGGCTGTACTGAAAGAGGTCCTGAGGGTAGCAGCTGTCACACTGGAAAGGGGAGAGTTACAAGACTCTCAGCTCTAGATTGTCAAATTTTACCTCACCATCGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGTGTGTGTGTTTAAGTATGTGTATGTATTTGGGGAGCAGTGCTAGAAATTGAACTTAGGGCCACATGCATACTCTACCCTCAATCCTGAGGATTTTACCTTTTAATTTTAACTCCTAAATTTTATGCTTACTTTGTATCATTTATGAAATCTGACCTATATGTAATTTAACTTTAGTTTTTTCCTGCCAGGATTTCTCAAATTTGCTACAGTTAGATATGTTTTCTATTAGAGGTGATGATGTTACATGAATATTGTTTATATCTTGCTGATTTTCAAATATAATATAATATAAATACTACTCTGAAATAGGAGAAGTTATAGAATGGCAGAGTGTAGTCCATCTAGAACAGAGTGTGTGCGTAGACTATCTGGCAGATTACACCTGGCAAGGTTGAATCAGAGACCAATGGCAGTACATCTCAGTGGAAGAGATGCTTAACATAGATGAACCAAGAGTTTCCTTTAAGCAGGGCTGTGCACTAAGTAACCCTTGTCAGAATATCAGCAGAGTTCCAAAGTTCTGAAGATACTCACAGTGGAAAGGTTCACTTTTTGTTTTCGTTCTAAGAAATATTTTGACATCATGCTAAGATGTGAGGGAGAGTTTGACTTTGGAGAGCATGGTAGCCAAGTTGGCTACCACACCTAGTACAACGCTTCCCAGTTGTTCAGGCAAAAGAAGAAGCTAGATGAGTTACACATGATACTTGGTAATTGTAGGCAAAGCAGTTTATTTATATGTAATATTCTCTCAGTCTAAATTATAGACTCTACAATGGCCAGTTATGTATATCCTTGATGCTATACTTTTTACTTGGTGTAATAGAATAATATAGGTAAGTATGTGGTTCAGATTTAACAAGTTGAGGAAAGATAATAGATCCCAGACTATTTGAATGTTGAATTTTGCAGGATCATCAGATGTCCCTGTAAGAACAGGTACACCAGTCTATTAGACTGTGTGTGAGAATAGCGTTTGGCTTTCTCATCTGACTTGAGTGGAAAACTTGCACTCCTGGGGCCTTGAGTTGCCCTTGTCTGTTTCTCCTCCCTGGTGTCTGGATTTCTTCCCTATTTCAGACAGTGAAGGTTCTGCTCCTGCTTTCAAAGGTGATGTTCTACCTGATGCCCACACGGGACTTTCTCTTTCTCAGTCTAGAGCACCAACAGAGACTATTCTCTCTGAGAACACATTGAACCATAGTTCACAGCACAGATTACAGGGCTGTTTCTCTCCTGGATATAAAATGTAAACTGCCTTCTGTTTCTTTTGCTTCCTGGGCCAG
Seq C2 exon
GCCAACCTGGGGAACCTGGATACGCTAAAGATGGACTTCCAGGAAGCCCTGGTCCTCAAGGAGAGACAGGACTAGCTGGACATCCTGGCCCTCCTGGTCCTCCTGGCCCACCTGGCCTGTGTGACCCCTCCCAGTGTGCGTACTTTGCCAGCCTTGCTGCCCGGCCAAGTAATGTGAAGGGCCCATAGAAGATTCTAGATCATCAAAACACTACTATGGATTTCTGAAACTTGAACTCGGAGCCCATTGGGAAGCCAGAAGCCTTGAAACATTTCAAATCCTTCTTCTCTCTCCCCTTCCTACTTCCCGCCTTTTCTTCCTGCTTCCCCTCTTTCTAGTCTTTTCTCCTTGCCTGCCTTAATTGTCTTTTCCCGTCCTCAGAGACCTCACAGTTATTAAAACCAACAGATACTGTCAGACAGTCAGGTTATTATTAATATTATTGTTATTGTTTGCTGTTATTTCAAAGGCTAATAGTTTTGAGGGAGCTTCCTGGTGGACAGGAAGCAGTTTCCTGGCTCAGCTCCCCTGTCATCACTGGCTGAAGTGTGACAGCCAATTTCTGAGGAACCCTCGGTGCTATGCAACCCTGACCATGTATGCACTTGTTGATTTTACCTCTTTCCTGGAAAGGAAGCTTTAAGGGATGGAGACTGTATTGTTGTTTCCTCAGCTGTGCCTAAAGATGGCCCAGGGAAAAGTAAGTTTGAAATCCCCACCTCTCCAGAGAGACTTGAAGCAAGAAGAAGAATTTGCAGCCTAAAAGAATTCATTGACCTCTGGAGACAAGGTGCACATCTGGAGTTCAGAACTGCCTCAGGGCATTGGGGGGAAGGTGGTTATCCTTGGTGCTTCAGGCTACCAGAACTCCAAAAGAAGTCACATAGTATTGGCAGTAGCTTGTGTCAGGGCCCTCTATGAACAAGCTGGTGCTGAAGAAGAGTTCCCAGGTGTGACTTCACTTCTAACTGTGGCCTGAACCCCTTCAAGTTCCTCATGCTGGTTTCAATTGTGTGAGTTGCAAAATAAAAGTTTTCAATGGTCACTTGCTTGACTTACTTGTGGGTGGTTCACTACCATGTACATTGGGACCTGTGTCAGTCATGCCTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTGTGTGTTCTGTACACACACCATGAACAGGTGATTACTAAATGTATTTCCCTTTCCATTGCTCCTGGGTGTTCATTCATTTCTGTTCTCTAGCCTCTCCTGGGCACTAGGTGAGCCTTCTTTGAACTGCAATACTGTGTCTTAACTGTTCTCTTCAGATGTTCATCACCATGCCCTTTGAGGATGCATTCAAATGTTTTGGCATATGGAAAGAAATCCTTTCGGCATGCTCAGGAACCACTGCAGACAGGGTCTGTTGCAAATTGGAAAGCTGACTTCCTTAGGAGGATTCCTGTGGACGCATGTCCTTACCTGCAGTCTGAACAAATCACCCTTGTTGATGTTCTCCACTTGGCTGAAGACACCGACTGATGGATGGACGGATGAAGCTGTCCATTAATAAGATGCTTTAGTTAGGGTTTCAATTGCTGTGATAAAACACTTGACCAAAGGCAAGTCGTGGAGAGAGGGGTTTAATTCAGCTTACAACTCTCAGTTCACACTCAATCACGGAGGGAACTCAAAGCAAGAACCTGGAGGCAGGAGCTGAAGTAGAAGCCATGGAGGAATGCTGCTTACAGGGTTTCTCTCTATGTCTTGCTCAAGCTGTTTTCTTATTCCATCAAAGACTGCTTGCCCAAGGAGGGGACCTCCCCCAAGGAGCTGGACTTACCCACATCAATTATTAATCAAGAAGTTGTACTACACAATGGCTACAGGCCTGTCTTTTTTTTTTCAATTTTTATTAGATATTTTCTTCATTTACATTTCAAATGCTATCCCATAAGCCCCTATACCCTCCCCCTGCCCTGCTCCCCTACCCACCCTCTCCCACTTCTTGGCCCTGGCGTTCCCCTGTACTGGGGCATATAAAGTTTATAAGACCAAGAGGTCTCTCTTCCCACTGATGGCCGACTAGGCCATTCTTCTGCTACATATGCAGCTGGGGACACGAGCTCTGGGGGTACTGGTTAGTTCATATTGTTGTTCCACCTATAGGGTTGTGGACCCCTTCAGCATCTTGGGTACTTTCTCTAGCTCCTCCACTGGGGGCCCTGTGTTCCATCCAATAGATGACTATGAGCATCCACTTCTGTATTTGCCAGGTACTGGCATAGCCTCACAAGAGAGAGCTATATCAGGGTCCTGTCTCTCAATTGAGATTCCCTCTTCTCAAATGACTCTAGTTTGTGTCAAATGGACATAAAATTAACCAACACACATGTCCACTCCTCCAAGTGACTGGTTCCTCACAAAGTTAAACAGCATTAGTTCACCAAGATACTCTATTTTGCCTCTTGATTTAGACACTTTGAATTGGTTTAGGAACCAGAAATATAAGCATCCAAAGAAGGCTTAAAGATTGATTAGGAAGAGAAATATTACTTTAGTGATTTTAAATTAAGATCCAAGATCTATTCCTTCTATTAGGCAAGTTGGTACTGGTGCAGAAAAGTTGATTTGGTAGGGTTGAGGTAGGCAGCATCCATCTGTGCAGGAGAGGTTTTCTCTGGAGCCTCCTTGATATCTACTAGCTCAGTTGTCTTCAACACAATGTAAGATGCCAAAGTAATGTAATATTTTTGTTTGAAGGAATATCAAGAACTCAGAACTCTCTTCTAGTGATCATGACCCAGAACAAGAGTCACATGTAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAATGCCAAGAATTTGGGGATAAAATATTTACCCTGACAAAACATGGCACCCTTTAACATTTATTTTTATTTTATTTTATTGTTAAGAGAAATACATTTAGGGGAGTTTTTACTCCACTGAAAAATTAAGGACAAAGTGTAATTTCCTATGTATTCCTAGTCCCCCTATCAAAACTGCACTGTAGGATACACGTGTGCTATAGTTGATGGACCTAGACTCTTAGTAACTGTAACTCACACCTTATATTTTGGTTCATTGTTGTACTCTGGGTTTGGTCTGAAGTACAGTGACATTTACCCACCAGTATAGGTTCACAGAGAAACTTCATTGTCTCAAAAAACCTGTTGTACTCTACCACATCATTCCTATATTCTCCCTAACCCCAATAATGATGGTTTTTATACCTTTCCTGTAGTTTTGCTTTTCCCAGAATGTCATAGTTAGGGTCCTATAAATTTAAGTCTTTTCAAACTACCTTCTTTTGCTTAGAAATATACATTTAACATTCTTCTATGACTTTTGTGGCTAGGTGACTCATTTATCTTTATTGCTGAATAATATTCCATTGATTATAGTTGCCATAGCTTTTATATCAACTCTTCTACTGACTGCCATCTTTGTTGATTCCTATTTGTAATACTTATAAATAAAATCCTTGTAATCATCCATTAATTAAATATGAAGGAGTGTTCTTGTTCCCATTTTATGTGGTCAGCATTTTTCACCTTTGCTCTGTATACTGCTTTTTTTGTTTAGCAGTTCCCTGATGACATAGAGGGGCAAGCATCTTTGTCCATTCCCATGTATTATGTTTTCTTTAACAAGATGACTGTTCATAGAATTTTGCCATTAAAAAAAAACCTGTTTTTCTTATTGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079022:ENSMUST00000159993:63
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(23.3=51.9),PF0139113=Collagen=PU(24.1=51.9)
A:
NA
C2:
PF0139113=Collagen=PD(74.1=68.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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
- 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