MmuINT0039732 @ mm9
Intron Retention
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:62906103-62914722:+
Coord C1 exon
chr4:62906103-62906156
Coord A exon
chr4:62906157-62914677
Coord C2 exon
chr4:62914678-62914722
Length
8521 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
ACAATTCTTCACCCCCACAGGGA
3' ss Score
8.62
Exon sequences
Seq C1 exon
GGCAACATGGGCTTGCCTGGGCTCTCCGGAAATCCAGGACCCTTGGGAAGGAAG
Seq A exon
GTAGGACTTGGTTCTGGGCCTGGCCTTGGCCATGGGCTTGCCAGCAAGCTTGGCCTTCACCAGAAACAACGTGGGCCACCTGGTTGTCGCTGGGCTCCCTGGGCACAGAGCCCATGGGCAAGAGATAAGAGGTCTCTAAATCCTGAGTGCAGTGGGGTTGGGACCCCCTTGGTATGAAGTGAATCCCCTGTGGCTAATGAGGTGTGACTAGAAGTGTCTCTGGCTCACTGTATCTCGGAGAAGGGCAGCCCTCAGGCGTACTTCAGGGGGTTATAGCACTGTCTGAATTTCTTCGCTGGCTGAGTAGTTTTGGAACTCAGTGTCCCTCCTCATGTGCAAAGAGGACAGAGACTCTCTTATCAGATCCTCACTGCCTGGGGATGGCTATGTGACTCAGAGGAAGGGTCTGAGGTCCACCCTTCCCTCTGAGACTGATTCCTCTCACTGATGGGCTACAGGACACACTCTGCAGAGGACACACATTCCTTGTGTGTTCCATGCAGTTGGTATGCTAACATGGTTGTTATACCTGCCATCTCTTCAGCCATTCTGGGTCTGCTCTTGGCTGGTGGTGATGGGCTTCTGCCACTTTCCAGGCTGGGACCTCCAGATGCCTTGGAGTCCTTCCTTTGTCCCTAGCCAGCTTCCCCCTATCCTTCAAGACTAGTTGTGCCTCTTCCTTGAAGCCTTCCTGGAACACTCAGACTGGACCATTGTGGCCACTTGTTCAGGGACACTTGGGCCATCTTTGTTGTTTTCAGACTTGAGTCTTGTCTCACTAACAGGGTATGCACATTGGGTTTATGACTCGTTTTTTTTTTCCTGGCAAGACATGTAGCTTGTATACAAGAGGTATCCTGGACAAGCAGGAAAGACAGTGTAGGCCAGAGACCAATCACTTTCCAGGAAGATTCCCTCAGTGCTCAAGAGCTGTCCAACAGACATGTGGGCCCAGGGCTCACTCTGGTTCCCAGATGTGGCCCCAGCTGCCTGCCCCCTAGACTGGTCGTCTGGTTTTCAGTGGGACAGCCAGGGTGTCTACTGGTCCCAGGCTGTTCTTTAATTTGAGTGTCTCCATTACACGGGGAGTTTGGAAGATCATACCTGTCACTCCCTTTTCCACTACCCTCTGTGGCAGAGCAGTCTATAACTTAAATGCTAGAGGCCAGCCTGGCCACTGAAAAGCAGAGTTTGCTGGCTCGGTGCATCTGCCTCTCTGCATGTACCTGGCCCCTGTTCTAGCGCTTTCTAGTGGAGGAGCCACGAGTGGGAAAGGACCCCCTGTCTGACTCCTAAAGCAGCCTATGATGGTCTCACTTTAAATGGGGTAGCAAGGCAGCAGAGGTGGTGGAGGAAACACAGGCTTGTGCCACCTCCTGCCTAGGATTCTGGGACTCCCTGTGCTCAGAAGATGGCCAGGGATGCTGACAGTCCCTGCTCCCTTGTGCAGGGTCGGGCATCTTCTGAGTTAAGCGAGCATCTTCAGTGGTTGGGAAAACTGCTCGGCCAAGTGCTCTGTGCTCCTCTCTGGCCCTGGCCCAGGCAAACACTTGTGGGCATTTCTTACAGAGCCTGGGTCTAAAACGGCCAGGGTGGTGTCACCATGTGCTGTGTAGAGCACAGATGACTCAGGCCCTGGGGTAGGGACCCTCTAATAGAGGTGGTGTCCTAGAGGAGAATGACTGGCTTGCTCTGTTCCTGGGCTTATCCCTATAATCAGTTCCCCGTCTCTGGTGACTGTGGCAGCCACTAGGGCCTGCTGCTCCAAGGTGACTTTGTCTTCTCTGTGGGAATCCTGAGGATATGGAACACCAGTGAGCAGAGGTGAGGCCAGCTATCTGCGGCATTAAATTTTGGTTCATCCACTCGTTCGATGAGAATGTATTAAACACCCACTGTGTGCTGGGGCCATGCTGCATGAAAACAGAACCTGCCTTACAGATCTTGCATCCTTGAGGGGCAGAAAATTAAAAACAAAAACAAACAAACAAAAAAAAAAAACGGTAAAATCTAATGCGTGTTGGTGGATAAAAAGGGACTATGGAGAAAGTGGCAGGAGAGAGTTCTGGTTGGGAGTGCCAGTGAAAAGCAGGTAGCAATTAAAAGCATTAGAAGGCATGACTGGGGCCACCTTTGACAGTAAAGTGCTTGCCACAAAAGCCTAATAACCTGAGCTTAATTCCTAGCACCGTGTGACAAGCCAAACGCTATTGGATGAACTTGTATCCCAGAGCTGGTGAGGTGGAGACAGGAAAGACTCTAGAACCCATTGTCCAGACATCCTGGACTAACCAGCAAGTTCAAACAGCAATACAAGCTAGGTGTGGTGGCACACACTTATAATCTCAGTATCTGAGAAACAGGGACAGGTGCCTCTCTGAATTTGAAGCCAGCCTGGTCTATATACAGAGCTCTAGGTTAGCCAGGGCTGCATAGTGAGATCCTGTCTCTAAAATAAAATGAACAAGGACTTCCCTTGAGGAAGGTTGATCTCTGGCCTCCATATGCATGCATGCATGTGCACACATTTGAACCTGTACCCACACACTTAAACACGCACACACATACATACTGCTGCTATATAAAGTAGGCAAAGGCATCTCTGTTTCATAGCTAAGAAGACCAAGACCCAACTAGATCTTATTTATTCAAGTCACCTTCTTGTTGGCACATAGGGACTTATGCTCTAAACCCTGAGTTGACCCTGGTGTTGAGTGACAGGCGGAGTTGTCAGAGCTTAGGGGTATTTTCTACAATGGTGACTCTCAACACTGCTGAGTGTTGATGTCACTGTGGGGATTCTAGGCTAGGCACTAGATCCAGGTAACAGAACTTCTAAAAGGCCCCAGGTGGGTCCCACATGCAGCCAAGATCCAGAGCCACCAACTTAAGGGAGAAATCTTCCTTTTGTCTTAAAGCAGAAGGCTGGGGTCTGAACCTGGGTCTTCTGACCCTTGGGCCCCTTTTCTTACCACAAGGCTGACTGTGTCAACTAAGAGCAGATTCACTCAGTTCATTTGAAGACTGTTCATCTGAATGGAATGTGTTGGAGTCCCAGCTCTGCCCCCTGTGGCTGTGAATGTGGGTGATCCACCTTTGTATGCTGAGCCTCCACTGTCCAGTGGATGGTTGGGGAGGTTAATGGGACATTCTGGCCCCAACATTCACACAGGGCTGGCACATGACAGGCACCATATATACTGGCTGGATGAATGAGTGAGCCAATGAATGATGATGGTCCTGAAAGAGAAACAGCTAAAGAATCCATGCTCATCTGGTGTCATTAATCCTCTGGCTATTTCACAGCTCACCAGATAAGCGGCCCTTCCCACCCTGCATGGAGTCTGGAGGCTCATCTGGCTGCCTTTGATTGTTGTGGATGTGAAACTGTCCCCCCAAGACAGGAAGGTCTACAAACATACTCTCCTGTCCAGGCTGGCCTCAAAACTTACAGTGATCCTTCTGTGTCAGGGTCCCTAGTGCTAAGATAACAGAGACAACCGTGCTTAGCCTCAAGAAGGTGGGAGGGTTGTAGCTGCTCACATGTGGGCGCTAGATTGGCTGCTTAGTCCAGCAGGGCACTGGGCAGTCCCAGCCCCCAGTGTGCACCTACAACAGAGGCTGAGCAGGCGTGGCTTGGTCCCTCACTTCATCCCCAGTGCCCCTGACTCCCTGTGTGGCTCTCTGCTGTGCCCCTGGCCTGACTTCTCCACATCCATCATTAATACTATTTGCTTCTCTTCTCAAAGACCCTCTTCCCCGAGTCTCACCTTTCTCAGACTCTGTGGCTCATCTTCTCAGTCTCCTGGGGATTCCCCATTTGCTGGTTCTTGAGTAACTCGCTGACACCCTCAGCACATTTCTTCAACTGGAGCAGGGCTCTGAGGTCAGACTCCTGCATGACCAACCATCGAAGTTTTCCTTACATGCGACTCAGCACACACTGGCCACCTACATCTGCCTGGCCCTACCACACCCCTACCCCCTCCAGTACCTCTGGCCGACATCTCTGATTGATCTGTCTTGCCAAGAGCTGATAATAGGCCTCTGAGTCTCAGCACGCTGTGCCAGGCAGACATGACTAATGGAAGGAAGTTGGTACAATGAAACTCATTTCTTTTTGCAACATCACATCCCCAGGGTCACTCGTCCTCCAGTACTGCCCAGTTGGCCACTGCCCTTGGAAAGATGGGATAAAGATAGTGGTCCCTGCTTTTCTGAGAACCAACTGTTCCTTCGAGTGTGACACCAAATTCCATGCTGGGCTCTTATGGCCTCTCTCGTGTTACAGCCCATTTCTACCCCCACCTCTGCCCCTCTACCTCACTGACCTGATGCCCCACTGCCCCAATGCCTCAATGCCCCACTGCCCCACTCAGGATACTGTGCAACATCCCCCAGCTGAGCTTTGTGATCTCAGGCACTCAATTCTTTACCAACATTCTTGTCCATATGCCCTTAGCGTCCCTACCCTCTTCTAAAAGGTAGTGACCACATTGCTTTTGTTCAATGTTATGTCTACTACTGTTTGCTCCCTGGGTTTTGATAATGGCTGAGGCTCAGCAGATGTGTGATGAATGAATGAATGAATGAATGAATGAATGATTACATCAATAAATGAACTACATGAAAATTCGACCCTCCTGCCTTCCCTTCCTCAACTTACCACCAAGTGGGTTGGATGCCCTGCAAGCTGTCTGATATTTCTAGATGATCTACTGATTTCAGAATCCTCTAACTTCGGAGCCCATAAGACATGTTGAGAAATCAGTTTGGGAAACTGAGGCTCAGAGAGGCTTAGTCTCACTCAGTTTCTTCTTATTTGCTCTTCTTTGCTGGTGGGATATGGGTTGCTGGGGTGGTAGGTGAGTTCTGTGAGCTGGCCTCCCTCGTAATTGCCAGGGCCTGGGTACTGAGCAAGCCTGGGGAGTGAGTTCCACTTTCCTACAGAGATGGAGCCTGGGGGCAACAACCTATGCCTGGACTCACACTGTTTGCTATCCAGACCCCCAGGCAGTGACCGATCCCCTTCCTCCCTCCTTGCCTGAAGTCCAAATAGCACCCCACTGTCTGTGGCAGGGTGAGGTGATGTCTGGTTCCTCCTTGTGCTCTGTAAGCAGTGATTAATCTGGCTCCCAAACCAAAATAGAGAGCGTGCTGTATTATAAACACGGGGCCTGCGGAGGCCCGCCTGCCAGGCAACCACGGCCCCAGCTCTTCTGTGGCTCCTCTGCCTCCCTCGGCCCACCTGGCACCCTTCATCCACACACAGGAAATCACTGCCCTGGGGCCACCTTGTGGGATGGCTGGCCCCTGTAATTGCCAGGGCCAAGAGAAGATAATGGTTTAAGAGCCTCATGTCCCCAGCCCTGTGATTTAAAACTGTTTGGTAAACACTGTTGAAGGGGCTTCCAGGCAGCCCCCTCCGCACCCCACCTCCCACCTTGACTGTGTTCCCACCGGATTTAGAAGCTCATGTTCACAGTCACATTCAAGGCCCTCTGGAGTTCACTATTGAGACAGCTCAGTCCATCCCACAGTTCTAAAGTCTAGAGAATGGTCTAACCTTGGCCTCAGCTTCCTGACAGCCTATCTTCTCCTGGAACCTCAGTCTCTTGTCAGTCCAGTGAAGCAAGAGATGGCCAAAATGGTGACTTCGGTCTTATCCAATGTGGGAACTTCATTATTCTGCTACTGACCTTTGCCCTAGGATGTTGCCATGACCAAAATGGCTCTGTCTCAGGGAGATGCATCTTTAAGGGGACCTTTCTTCTGGGCTAGTCCCAACCACAGTGATTGATGGTTAACATCTGAAAGATTTTGGGCCATAATCCACACACTCTCTCATGAAAGCTGTGTGGCTTCAGGATGGCCCCTAACCTCTTTGAGCCTCCTTTTCCTCACTGTAAGTGTACCAAGTGGTACCTATCTCTTAGAAGTGATCCAGGGTGTTAGTGAGCACGCATGCTTAAGGCACGGGGTTAGGCATGGTGGGTTCTGTGATTCACTTCCTTCCAGCTCTTTCCTGAGCATAGGTTTGCTTAAACCTCATCTGGGATTTAACTGAACACATCCCTTTTCTTTAGGGGAGAGCGATGCTGTGGATTGGTTTTCAGGAGTCTTGGGGTGCTAGAGGCTCCTGCCTCACACTGCCCCCATTGTTGTTCTTGGTCCCCGAGACTCTGGGCTGTTTACAGTGATCCTCTAGGCAAGCAAAGCTTGGCAGAGTGAGTTCAGAGAGGTAATTGCCGGGGTTCGATCTCGCAGCAAGAGCGCATGGCTCACCTTGATGCTTCTGTGGGAGAAAAGGGCCTCAGCTTGTTCCTCCTCGTATCCTGTCATGCCCTGTCCCCTTGTCCCTAGGGTTTCCTGACACAGCTTCAGTCGACGGCTCTGACCTCCATCTGCCTCTCTGCCCACTGCCCTTATCTGTTCTTTTGCAGTTACATAGGCCTTCTTGTGCTTCTCAGCTCGCTTCTCAGCATCTCTGCCCTGGGGCTTCTGTACCCTCTGTTCCACTTTTCAGGATGCTACCTCCAGGTCTGTCTACCTTCCCCCATCAGCCATCCCTTGGCTGTCCCTGGAGTCACCACCCCTCCCCAGGCATGCTGTCCTCTGTACCCTGACTTTATTTGTTCGTGGCAACAAGCCGTAGCATCAGATTTGCCATTTCAAACCATTTCTCAGTGCACTGGTGATGGTGTTCAGCACAATCGAGCGATTGATTGTTGAGCAACTGATCCCCGGAACATATTCATCTTGCAAAGCAGACTCCCGCTGCTCATTGCACTGCATCTCCTGCCTCCCACCACCTACGCTTGCCTTTTCTACTTCATTTCTTTCTAGTTCCTTTCGAGGAATGTAAATTCTCGAGGCAAAGCATGTTGCCTGGCTCCTTTTTCCCATGAGGAAAAACCTGCTGGCCCACGCACACTCCATCACTGTTTGTTGAGTGAGTGAATGAATGAATGAGAAATGAAAGCCATAGTAACAACCGTAGCTGGTGTTTCTAAGGTTGCTGAATTCAGTGCCAGACACCACGATTTGTGCTTCCTACGCAGATCATGCCACCCAGGCATTGGCTCTTCCTGCCCATTTTATAATTTCTGAGGAAATCAAAGTTCAAAGAGTCATTGTCTCTGGCCACATAGCCAGCCCGAAGGCAAACAGTCCTGGAATCCAAATCGATCTGTAATAAGAGCGGAGATCCTTTTGTCTAGCTGCTTGCTGTAGTCTGGGGATCACCTTGCCTACTTGTGACCCAGTGGGGGATTTTTTCCTAGGGGCAGCTCTTGATCTAGAGTAAGATGTGTTTCGTGGGTGGTAGTCTCTCTTGGCATGAGACGATTCTGAAGAAATGCTGGCGAACTTCCCGAGCCCCCTCCCTAAGACAGATTCTTCTGTTTGTAATGAAGACTGCGACTTCCTATGCATCCAGGATGCTGACGGACACCTGTGTGAGGCTGTGTTTATGTGTCTGTAGAGCAAGTGCGTTAGGGGGCTGGGATGAAGGATCAGCTGGTAGAGTGTCAAGCATGCTAGAGTCCTGGGTTTGACTCCCAGCATCACATAAACCAGCTGTGGTGGTACAGGCCTGTAAGTGAAGGCCTGGGAAGTGAAGGTAGGAGGAGCAGGTGGCCAGTGCCATCCTTGGCTACATGGGGAGTTGGAGGCCGGCCTGGGCTGCATGGGACTCTCTCTTAAAATAAAAGAAGAAAGGAAGGAAGGAAGGATGGATGGAAGGAAGGGAGGGAGGGAGGGAGGGAGGGAGGAAGGGAGGAAAAAAAAGAAGGGGACAGAAAAGAGAAACAAAACAGAAAGAAATGAGGTGGCGTAGGGACTTATGTCAACCATGATCTCCATATGGCCGGCTGTCCAGGGCCTGTGCTGATTGACTTACTATCCCTTGTCATAGACTCTCAGGGGCCCTAGAACTTAGAGTTAGAAGATAACAGAACCTAAGGGGCCTCAGAGTTTCAAATCCCCCGTTAGAGGTCCACAGAAGGTTGACGATCACACACTCAAACATGCACCGTAAGTCAGGGGCAGTGTCTCTCCTAAACAGAGCCCTGGTGTGAGAGGCCTGCCAGGCGGCAGCCTGGTGTCACTGAATGAAGATGAAGAGTCAAGGCTGCCACTGAGCATCTGGGCAGCCTTCTTCTCCTTGGAATAGGAGCAGAGCCAGCAAGGAAAGAGGCTGTGTCTCTAGGTGATATGGTCATGGTACATGAACTGGAGTGGCAGATACCGTGTGTGTTCCAGATCGCCCTTGTCCCTGTTCCTTATGTGACAGACCCTTTGCTCCTGTTCCTGACTGCCTCCAACTTTCTGAACTTCCAAGGCAAGGCTGGGATGTGGACCACTGGGTCATAGTCTCTCACTCCACCCCCATCCTCTGCTCTAACAAAAGATGACTCCAGAGGATTCAGTGAACTCCATCTGGCCTGCATCCATGCAGGAAGTGTGTACCATATCCCTACCATAAAGCCTATTGCCTGATGACAATTCTTCACCCCCACAG
Seq C2 exon
GGACACAAGGGCCATCCTGGAGCAGCAGGGCACCCTGGAGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672-Col27a1:NM_025685:7
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(25.8=100),PF0139113=Collagen=PU(2.2=11.1)
A:
NA
C2:
PF0139113=Collagen=FE(21.2=100),PF0139113=Collagen=FE(15.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: