MmuINT0039088 @ mm9
Intron Retention
Gene
ENSMUSG00000022371 | Col14a1
Description
collagen, type XIV, alpha 1 [Source:MGI Symbol;Acc:MGI:1341272]
Coordinates
chr15:55349737-55352358:+
Coord C1 exon
chr15:55349737-55349892
Coord A exon
chr15:55349893-55351487
Coord C2 exon
chr15:55351488-55352358
Length
1595 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
CCCCCACTTTTCCTCTTTAGTGT
3' ss Score
10.38
Exon sequences
Seq C1 exon
GACCTTCAGGGGAAAGTCGTCCTGGAAGTCCTGGGCCACCTGGCTCTCCTGGACCAAGGGGTCCCCCGGGCCACCTGGGAGTACCTGGACCTCAGGGTCCTTCTGGCCAGCCTGGGTATTGTGACCCCTCCTCGTGCTCTGCTTATGGCGTTGGAG
Seq A exon
GTAAGTGCCAGTCTCTTGAGGGCTTTGCCCAGTTATACAATGGTTAATACTAACCTGTGTGTGTGTGGGGGGGTGGTGGTGGTGGAAATTAAACAGGGAGGGCAGCAGAACCTGGGCTCCATACTCCCTTACATCATCTTTAGAGTGCAAATTACTGCACAGTCTACTCACATCCCTTAGGAGAGACTTAAATAACACCGCAGCCATGTTTTCTTTGCTTCTAAATGTTGATTTCTGGACTGAGGATATAGCATATTGGTAGAGCATTTGCCAAATGGTGACCCATAAAGACTTGGCCTCCTAGTGGGTCACTTGTCACATATGGTTGAACATTTAGATATTTTCCATGCTGTTTCTGTTATGGTGTGCCCGTGACCTCCTGCAAAATTTCACTCTCTGTTTAAGTTCTCCCCCCATAATAAGCGAGGTCCCCAAAATTCTTTTAGATGACATCTGCCCACCATGTGACAAGAAAGGTCTTAAGATCAAAGTTGCCAGCTGTTTTTGCTTCATCACTAAGTGATAGGCTGAGATTTTGAGAGCTGAAGCATCTCCCACACATGGCAGCAGTCTGCCTGCTCACCCTGGGGCCTTTCTGAATTATCGAGAGAGAGGTTCAGAGACCCGCTCTAGGTCTGTGAGGAGATTAGTCAGCAAATGCACGTTTTTCCTTTTTAAGAGAAATTTAACCTTAGTTGCCAGAGAAATTGGTCCAAGTTTTGTTGATGTGTTTTTTTTTTTTTTTTTCTGTTCATCTTTTCCCTCCCTGTCCTCTCAAATCTGTCCCCTGTCCCTTAAGATCTCATCCCGTACAATGATTACCAGCACTGAAGTGCTAATCCTGCCTTTGGTTGCATTGGCCTGGGGATTTGGCTATGGATACACAAGTGGTTCACCACCACTACTAAGCTCCTGCCCCTGACTGTGGTCACCTCTTTCCTCTCTCACCTGCTTCTCCATCTCAGACTTTCAAGTCCCCTGCCTACCCGGCTCCAGACATGCTGGAGTGATAACATTGTAACAAAGTATAACAAAGTGCAACAAAGTAACATAAATCAACCATAGTAGAACCAGACTTCCGGTCAATCTGAATGGAGGTCTGGGCCTCTGAACCAAGACTCTATCCCAAAGGCCACTTTACTGAGGCTCTATCCTGTTCCACACAATAGGATGAGTATCTTCCTCCTGGCTCTTTTGCTCCACCTCCCTCTCTTGGCATCCCCTTCTTTCCACTCTCCCCTGGTGATGGACTTGTAACACGAGACTGGGTTTTTAATTTTATATTTTCTTCTACGATTCTACTGTATTTCAGGGTTTCTTTTGTAAATAAAAAACATCCGGTATTTAAGCAATTGGCCATGGTTCCAGTTTTCTAACTCCATTGTTTAGTTTGTCTTTCTCTTCCTCCTTTTAACAACTATAAAGCCTCCTGGGGAAGCGGCATAGCAGGCTCGGCAGTGAGTGCTTTCTCCTCACACATTGCACCTCTCTGCTTTATTGACCAAATCTGTGTCCCTAAGGACCCAGATAGGGGAGATTATCCATTTATGGTTCCTGGGCCCCATCAGTACCCCACCCCCACTTTTCCTCTTTAG
Seq C2 exon
TGTCCCATCCTGATCAGCCTGAGTTCACACCGGTCCAGGACGAGCAGGAGGCCATGGATCTGTGGAGCGCAGGCATCTGATGACCTCAGGAGACATTTGAAGAGCAGGGGCAGGCCCTCTTCTGGAGCTTCACTTACCAAATGCTGTCACGTGGTTTGTCCTCTACTTTGCAGAGGGAGGCAGGGCTGATGGTATGGGGTATATTTCCTCTGTGGATAACGTCAATATTACCGTTTTTTAAAAATTGTGTTTTGAAACCGCCCCTTTCTGTGACACTGTTTTAACTGTACACCAGTTACTTTGGACTTCTTCCAATGAAGAGTGCTGAGAAGGATACACCCTGGAGTGTCTTCTCTGTTACATCATTTCAAGTTGTAAAATTAATAAGAGAAGCGTGGTTATATCAGAGGGAATTTGGGGCCCTATCAGCAGAAGAGCGAATTCAGAGATTCCCAGTTTATACCACTGTCCCTGTACCCATGTCAGTGACCTTGCTGGTAATTGAATAACACCATCACTGAGGAAACTACCTCCTACTTGTTTAACCTGATCTGTCTAACTCATAGATTACTCAGTAACTGGTTTTCACGGGTGTTCAGAAATAAGAGCTAGAATATAGCCTTTCTCGATTCTGTAATTAAAAACAAAACCATAGAGTCTGTTTTCCAGTAGTCTTGATTCGTATAAAATAATGACTTCCTTCCAGTTCCGATGCAGAAAAGACCCATCTTTTGGCAGATCATTTGTCCAGGAGTGTGTTTCAGGGCTTGCCTCTCCTCGACTTACAGGGATTGCTTTGTAAATGCAGATATGTTTTTGAAGACTTGTTTTTATCCTTTTTTTTATAAGCAAATAAAAACTTAAAACACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022371-Col14a1:NM_181277:47
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.991 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(75.0=79.2)
A:
NA
C2:
NO
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:
CTGGGAGTACCTGGACCTCAG
R:
AGGGGCGGTTTCAAAACACAA
Band lengths:
347-1942
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: