MmuINT0039565 @ mm9
Intron Retention
Gene
ENSMUSG00000063564 | Col23a1
Description
collagen, type XXIII, alpha 1 [Source:MGI Symbol;Acc:MGI:2653243]
Coordinates
chr11:51393077-51397427:+
Coord C1 exon
chr11:51393077-51393115
Coord A exon
chr11:51393116-51393565
Coord C2 exon
chr11:51393566-51397427
Length
450 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCG
5' ss Score
9.67
3' ss Seq
ATCTCTCCCTCCTTTTCTAGTGA
3' ss Score
10.77
Exon sequences
Seq C1 exon
GGCCCCGATGGGTTGCCTGTGCCTGGTTGCTGGCATAAG
Seq A exon
GTACCGTACAGGAAAGGGTCTCTAGGGTGGGCCTGGAGGAGTTGGAATGAGAGAGTTAGAGAGTCAGAGAGGACCCATGGGGGACCAGGCACCATCACGAAGAGGTTAGAGTCTCTACGCTGCTGTCTCACACAGTGACTGAACAGTCATGTTTCCCAAAGATGTTTGTGACTTTTTGGTCACATGGCCAAGGCTTAGAGCTTGGTCCTGGCTGATGTGTGTTATCTGCCTAGCTGGTCATCTGGATCTTGGATAGCATTTGGCCCTACCAGTTCAAAACCATCAGGGAGTTTCCTGGGACTTATTTTAGCTGTCCCACTGAAAGGGGTCTGGAAAGAAAGGGAGGCTATGCTTGTTCCTGAACACATCAGCAGGGTAGACGTAGCTAGTGGGGACCACAGGATCTCCCCAGACTCCTCCATCACCTTCCATCTCTCCCTCCTTTTCTAG
Seq C2 exon
TGATCCTCAGACATAACCCCTGACCTGTACAGATCCGTTTGGATGTTTTGAACTCATGTAAAAACAAAACAGTAATATATTGAACTTCTTTATGGGATGCGCCAACTGTGGCCATGTAACATTTGCAAGTGTGCCAACCAGCCCCTGGACAATCTGCACAGGAAGCCAGCAGGAATGCGGACAGGCTGCTCTGAGGAAACTTCTGTTCAAAGGCCCTGGGTAGGGCCTGGCTTTCCCAGGGAAGATGACGAGGGTGAAAACGCCTGGCTCAGGTGAGGCTGGACAGACTCCAGGTTGGGCTCATAATCACCTGATTAGCAGAGACTTGCAACAACTGTTTCCTGAAACCCCACTGCCCCAGCTTCTCACTGTCCAATAGCACCCCCTTGGACAACTGCTGTAGCCTCTTGCTTCGGGACTGTGCCGTAGGCAGCTGCACTGGGGCCCTATGTTCAACAGGGCCAGCAAAGATTCCTAGAGTCCAGCACTTGGGGAGAAGGCAATGGGAAGAACCCGAAGAGGGCCTTGCTCCACCCAAGTTCAGCACGCTTCCAGAAGCCACCCTGACACGGGAGCTTGTATTCTCGGACCTTGGGAAACAGCAGGCTCTGTGGATACCTCAGTGTAAAGCCAGCTTCCGACAGCCCAGTGAACCCTAATGGTAAGATGAAGAGACCCATACCTACTACTTACTACTTCCAGTCTCCTTACCGCCTCTCCCAGAGCAGGAACTGGAAAGGACTTTGTCAGCCTGGAGGAGACAGGCCTCTTGTTCAGAACTTGTGTCTCAAGTCTCCCACCTAGACCTCTGGTCAGCCTGACAAAAACAGGCCTCCTTAGTAAATGGTACGGACACCATGAACCTGAAGGCTGATCCCCCAGCAAGCCTGAGCAAAACACCTGTGACAGAAACCCCTGCCCTCTCTGGGGGGGATTGGGGCTTGAACACTTCTAATGAAGGTTCCTAGCTCCTGCTCCATTCATGGCTTCACAGCCCTCCTCATGTAAAGGCGCCATGAGTAATAAACCACAAATGTGTGTCTGGTGTGCCTGTCGCTTACAGACTTCCCTGGTCACCTCTGGGTGAGTTTTATTCCGATGGTTACTAGCTGAAGAAGCAAAGGGGCTCTCCTTGGGGGTCAGAACCTTCCTCTAAATCAGGGGATATATTCAGGGTAGGAGATAAGAAGATACAGGCTCAAGATCTGAACCCACACATGCCAGCAGAATCCTGGGACTGGCCACATCCTGTCACTGAGTCCTCTGTATCCCCTTTTGTTATGCTCAGCAAAGACACCCCAAATTTGTTGCCTCAAAATGTCCATTCTCTCAGTTCTAAGGGCTCAGGGGCTTGCCTGAATAGGCCTCAAGTGGATTCCCCCTCATCTGTCTGTCAGCTAGGATCCAATGACAATGACACCTACCAACCTGTGACTTTTCTGCATGGCCTGGACTTCCTCACAGCATGGCAGCAGGATTCCTAGAAAGCTGTGTCACCTCATATGACCAAGCCTTCAGAGTCACATGCTGCCACTTCCTGCCAGAGCCAGAAATTTACCCCACTTGAATTAGAAGACAGACCCACCTCTCAATGAGGAAAGTATCAACGTCATGTTTAAATGAGAAAATATGGGAGAGTACATTTCGTTGTAGCCCTCAAAAACAAAATAAAATAAAATTAGCTCTCTTGTAGCCCAGGCTAGCACTGAACTCACTATGTAGTTCAGGATGACCTTAAAGTTCTGGCCCTCTACTCCTTGCTCTATCTGCTCCAGTTACAGTTGTGCACCACTGTGCCTGACTTCTACAGTGCTGGGATTCAAACCTAAGGCTTTATGCCTGTTAACATAAGCACTTAACCAAAAAAGCTACAATCTTAGCCCTTGTTACGGCATCTTAAATAACACCACTCATCTGTAGCATGAGACAGTAATGCTCAAAATTCAGGTGTGGTTCAGTAAGATTCAGCTCTGTGGAATATACACAGAGAGCCTAGGACAGATCAGACACCTCACTGTACCTGTGGCTGGCTGTCCTCGCTCTATCTGCTCCAAGACCAAATAGTAATCACGGTCCTGCAGAGTGGGCCCATGTCTCCCCCTAACTTGTCCTTACAGCAAACTGAAGAAAGATGCCCAACAAATGTGCCCATTTTCATAGATGACAAAACCAAGCTCTTTCCCTGTGTGTAGAAAAGACAGGAGCGTCAATGACAGTGTCTCTGTCCCCTTCCTCCAAGGGCAGAGATCCAAGGAGGGCCACACTCCCCAGACTGTACACATGCATTCCTTGCTAAGCAGAGGCCCAGCCACACACAGCTGATGTCAAGTCCCTACCTCTGTCCCCCTGAGGAGCTGGCAAAAAGCAGCAGACCATGTTCTCTGCCACACTGGGTCAACTAGGAAACCAGATAAAAGAAAAAGAAAAAGAAAACAGATGTAGTGGACCAAGATGACTAAGGTGGCTCACTGGTAACAATGCCTGCTTTGGAGATGTGACATAGCCTCCCAAGCCCACCACAGCCTACAGTCAACAAAGCACTCCTCCTTCATCCTAAGAACAACATCGTTAGGGCTGCAGGGGTAGGTGTCACTGTGTCCATTTTACATATAGGAAATCTGAGGCTCACAGTGCATAGTTATCTGCTTAGAGATACACAGACAGGCGAGAGTGACAGGCTTGGGACTGAACCCGTGCTCTCGGAGGTCCCCTAATTTTTCTTCAGGGTTGTTTGGCAACATATGGAATCTGCTAGGCAGACCCCTGACGATGGGTGGACAGCACGCAGAGCTTTCTAGAGGCTGACGCCCCAAACTCTCCCTTTCACCTCAGGCTGCCCTGGGCCATTCTTGGCCCATTACTGCCCCCGTGTGGACTCATACCTTGTATCCTTGCAAATGGACATGCAGAGCCATGGAGTGTCCTGTGCCAGCCTGAAGTGAGGACAGAGAGAATGAGTTGTTCAAGGTCCCAAGTGAGACGCTGGGGAGTGCCCTGCCTCAACAATGAGGCTCAAGGACTGAGAGGAGGCCTTGGTTCTCCCTACCAAGAAGGCCAGTTCTCTTTGTAATTATTTGTAAGTCAAATAATTCTGGAAGGGAGGTATCTGTTTATTGAGTCCTTGACTATCCTGTGTTCCATGCCGCTAAAGAAACCAACGAGATGACTGTCCCCATGGACAGATGGCTCTGAGGCTTGAGAGAAGCGACCTTACTAGATTCCCTGTCCTTAAAGCTTTGAGTTGTCACAGGATTGGGGGACACTCCTGGCATTCAGAAGACAGTCGAGGTTAGCATACACCTGAAATCCAGGACACTGGACACGCCCAGTAGTGAAGCTGCTCACTGTGAATGCCAGCTGAGGAAACCCTGCTCTGGATTCAAGGGTTGGGCAGGGGAATGATTGCTTGTTGGTTGAGACAGGGTCTCAATACATAACTTAGGCTGGTCCCAAAGTTGCAGCTCTGCCTCAGCTTCCCAAGTGCTGGGATTACAGGCTTGCACCACCATGCCCCCCACTACATCCAAGTCTTGTTCAGTCCCTTCCTCCTTTCAGCCTGTGCCTTCTTGGCCTCCAGGGTTGCCTTGAAAGGACAGATGCCAGAAAATGGAGAGAGGATGGGACCAAGGACAGGAAGGATAGGCCTTTTCTGAGCAGGAAGATGGACTTTTAGGTAGGTTTATGGTTAAAAACATGAAATACCGCTCAGTTGGGGAAGATGGAAGGGCTCTGTGACTGGGTTTTGGTGACAAGATGCAACATTGAGAATGTACTAATGCCACTGAATTGTATGTACCCTTCAAAATTGCTTGTTTTTTTATGTATATTTTACCACAATAAAAACAAACAAAAACCACAAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000063564-Col23a1:NM_153393:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(4.3=23.1)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCCTGGTTGCTGGCATAAG
R:
ACAGTTGTTGCAAGTCTCTGCT
Band lengths:
358-808
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: