Special

MmuINT0040212 @ mm9

Intron Retention

Gene
ENSMUSG00000026837 | Col5a1
Description
collagen, type V, alpha 1 [Source:MGI Symbol;Acc:MGI:88457]
Coordinates
chr2:27854246-27857143:+
Coord C1 exon
chr2:27854246-27854299
Coord A exon
chr2:27854300-27857089
Coord C2 exon
chr2:27857090-27857143
Length
2790 bp
Sequences
Splice sites
5' ss Seq
ACCGTGAGT
5' ss Score
9.4
3' ss Seq
CTGCCTGACTCTCTCCACAGGGT
3' ss Score
12.36
Exon sequences
Seq C1 exon
GGCCCACCAGGCAAGGACGGACTCCCTGGACACCCTGGGCAGAGAGGGGAGACC
Seq A exon
GTGAGTATCACAAGTGCTGGGGACATGGCTGTTCCTGGCCTCTCTAGCTGGGTCTCCCACAGCTTACAATGCTGCTGGCTGCCTGGCACAGTCAGGAGCCCCTTCCTCCCTGGGAAAGACCAAAGGCCTTGGCAAGGCTTCCTGTAGGCCAGCCAATCTGCTGTTGACTTAAGGTCAGGCTGTAGGGTGGGCGGGAGCCCCAGGATGTCACAGTGGAAACCCAACAATGGCTCTTTGCATGTTTTAGCAGCTTTGCCAAAGGCCATGTTTAAAGCATCAGGACACTGCGTCGGCATCACAAAAACCTTTATTTTCTGAGGGTAACCGTGAGTGTAGCCTTGCTGGGACCATGGGCCTTACTTGGAAAAGTACCTGGGAGGCTCTGTACTTGTAGAGAGCTGGTTGTTTAGGCTACAAAACCTCATGACAAGGGCCATGGGCCTTGGGCCTCGCACAGACACCAGCTTTGTCCATCTGGGAGATTTCAGCCCTGGGGAGCTGGTGGGAAGGAGTGGAATGAAGTCTTTCGCCTCCTCTATAAAGAAGATGCTGTGTGGGAGAGATGGGATGGCTCAGTGGCCTGACTGGGCAAATATGAGCATCTGAACTATCCCCAGCACTGATGTGAAAGCTTAGCGTGCGGCACAAGTCAGTAAGCCTGGTGCTGGAAAAGTGGGCAAGAGGATTCATTCCTAGGACTGGCCAGCCAGCGAGGCCAGCCAGTGGGTCAACTCTGAGTTCAGGAAGAGACCCTGTCTCAAAAAGAGCATGTGCACATTTGTCGCCTTGCTTGCACTTCTGACCCTGTGATTCCAGACTTTGAGCAACTGAGCCCTCAAAGTGCAGGTGATACCCGTGCGTTCTCTTTGTGTGGCTCTGCCTTATCCATATTAAAGGCCAGTTCGTACCGGTGTAAGCGTTCCTCCCTGACAGGGTCCTGTGCCATTGCGTCCTGTTCATTGTGCTGGGGTTGGAGTGAGGGCTCTCATGGCTGAAACTGGCATTTCTGATGTGGGCCTTTGACCACCCCGTCTATTTCCTGGTACCTGCTTTAACATGTGTTAAAGTGTAAAGTACCTGCTTGTCCTTCTCTGTCTTTCAGCACACAGGGACGTGAAATCTTTTAATTACGCCTTTGCTGGTGTTCGAGCAGCCTGTGCTGGCTGATAAATGGAGAGTACCTTGCTCTTTTGTTTAGAGAGAAGAATTAAAACGTTTCTTCAGAGCTTTGCGCATTTTCCTCTAATGCCTTTCCAAGGAGACAAGAGAGAAGAGTTTTGCATACTGCATGCTTTTCTCCCTCAGACTCATTCTGCAGAAAATTAAGCCTCCTAATTTGCTTGGAAAAGTATAATTTCCAGCAACTTCTACCATGTCCAGCTACCTTTGTAGAAACAGGGGTGCTGCATGCCGCTGCTGGCCATCTTGACTCTCTCTGAGACTCGTTCGTGGTTCTCTAGAGTAGACTTCCTCGTTTTCTTTTTCCTTTCCTCCCCTTCCTCTTCTTCTCCATCTTCCTCCTCCAATGAACACAAATGCCGGTTACTTCTCCTTAACGGGAGCCAAAGCCTGTTTGTCAGTGAGGAACAGAAGACCATCTCCCTCCTTATCAGGCACGTCACCTTAGAGTGACTGTGGCCAGCCAGCAAGGAGAGCCAGTGCATCCATTCTGGGTCCAGAAAGAGACCCTATCTCAAAAAGAGCATGTGCTTGCCTGTGGCCTTGCCTGCACTTGTGACCCCAGGATGCCAGACTTGGAGCAAGTGAGCCCCCAGAGTGCTGGGGTATTCACTGTGTGCCCCCGCCTCAACCACAGGAAAGGGCAGTTGGGACTGCTTGCCCTCCCCGCTAACACTGCTGTAAGCAAAGCTTTGGCTCCAACCTCCTCTCAGACACTTCTCCCTCCTGACCTCTCCTTCACTCTTTGCTTTTGACCATCAGAGAAATGTATGTTAGAAATGGCCAGGTCTGCCCCCTGTGTGAGTTGTGCTGAGAGAGAAGAGCCCTCTGGGGTCTACAGGGCAGAGTCTGCTGAGGCCAGTGAATTGTGTGTGATAGTAGCTTGTTGCCTGCTGGCCCTGAGCCATCTGCTCACCCTCACGTCATAGTTATGACCTCTGCACAGCTAGACTGCCCTTGGGTAGATCCACCCTTGTACACCTGGCAGCTGCCAGTGCATCTCATTGTGCCTACTCCATCATCATGCCCCAAATCAAGCTTGACTTTCTTCAGCCTCCTGCTCCATAGGAGAGTTTGGGAAGCAGAGGCGAGTGGGAGGCGAGCCTGGGCCATTCTAGGCATGAACACTCAGATCCTCAAGGAGTCAGGGTCTATGAAGTGACTTTAAAGTAACACATTGGAGCTGACAGCTTCAGAGAGCAGTCAGACCCTGCTCCCACCTGTCCTAAATTCGAAGAGGAGCAGGCTGGCGAGTCACCTGCCGGGAGTCAGAGACGTGGATAACAAAGGCTAAAAAGTCCCACGACGTTGCTAATGAGCACCAGCCCCGAGATGGTTCTTATGTGTCCTCAAAAAAATGAACACGCGGTGACATGAGGGGGAATAACAGGCTTACAAATCCATTTCTCAGCACAAAGACACAGTGTGGAGCTAACCCTCTTGGCTCCAGTACTTTCATGAAATTAATATGAGAAGGGGAACATAAGGCATGACTTCAAACTGAGCGTTGGGCACACAGCCATTGGGGACAGGTGGGGGACGGGCTTCTGAGACTGCATCAGGATGGGGGTGCCGCTGCAATGGCCCTCAGCTGCCTGACTCTCTCCACAG
Seq C2 exon
GGTTTCCAAGGCAAGACTGGCCCTCCAGGGCCCCCAGGAGTGGTTGGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026837-Col5a1:NM_015734:37
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:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028280





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:134798462-134801953 
ALTERNATIVE
HsaINT0039254
(COL5A1)
Human
(hg19)
chr9:137690308-137693799 
ALTERNATIVE
HsaINT0039254
(COL5A1)
Rat
(rn6)
chr3:6542323-6545168 
LOW PSI
RnoINT0039979
(Col5a1)
Cow
(bosTau6)
chr11:106894619-106897435 
LOW PSI
BtaINT0041978
(COL5A1)
Chicken
(galGal4)
chr17:7536427-7539903 
ALTERNATIVE
GgaINT0125293
(COL5A1)
Chicken
(galGal3)
chr17:8218126-8221602 
ALTERNATIVE
GgaINT0125293
(Q90689_CHICK)
Zebrafish
(danRer10)
chr24:28737355-28738291 
LOW PSI
DreINT0048873
(col11a1a)
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
(Submit an annotation)

	


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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"