Special

MmuINT0039965 @ mm9

Intron Retention

Gene
ENSMUSG00000031503 | Col4a2
Description
collagen, type IV, alpha 2 [Source:MGI Symbol;Acc:MGI:88455]
Coordinates
chr8:11445960-11449287:+
Coord C1 exon
chr8:11445960-11446246
Coord A exon
chr8:11446247-11448058
Coord C2 exon
chr8:11448059-11449287
Length
1812 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGT
5' ss Score
8.35
3' ss Seq
ATCTCCTGCTCTCTCTGCAGCAC
3' ss Score
11.5
Exon sequences
Seq C1 exon
GACTGGCAGGCTCCTGCCTGGCACGCTTCAGCACCATGCCTTTCCTGTACTGCAATCCGGGTGACGTCTGCTACTATGCCAGCCGCAACGACAAGTCCTACTGGCTCTCCACCACGGCCCCTCTGCCCATGATGCCCGTGGCTGAGGAGGAAATCAAGCCCTACATCAGCCGCTGCTCTGTGTGCGAGGCTCCGGCCGTGGCCATTGCCGTGCACAGCCAGGATACCTCTATACCCCACTGCCCGGCTGGGTGGCGGAGTTTGTGGATCGGATATTCATTCCTCATG
Seq A exon
GTATGTATCCCTTCTCCATTCTCTGAGCATGGTACCAAGTGGAACCTTCCCCATCTACCTCCTAGCTGGGGCACAGAAAGGACACATATTAAATAAACCAGGGCTGAAGATTTGAGCTCCATGGGTAAAGTTTGGATCTCCAAGAACCATGGAAACACCAGTGAGGTAGAGCTTGCCATGCTGTATCTGTGCCAGGAGACAGACAGTGGGATCCCACTCATTCCCTTGCAGGCTAGACTATCCAAAAAGCGCCAGATTCAAGGTCCAACCCCCTTCTCAGAAGATGAGGTGGAAACCAATTGAAAACCCGTGACCTCCAGATAATCACATACACTAATCATAATTGGCAATTGCCCAAGTTGTGTGTCATACAAGCGCACCTAGTGCAGGAGTGGAAGGCTGTCATTCAGCTGGACCTGGGCTGAGCTGTGTGCTAGGCAAGGGGCTAGCTTCATGCAGTGTGAGGATCGATTTGCCACCCTACCTTTACATACAAGATGCAATGTTTCTGTCTTAGCAACAAAGTCTACACTTTCTGGTTTGCTGCAGTTTAAGTGAATGGAAGAATTCTCTTTCAGACTCTTTCTGGACTATAGAACACTCCTTCCCAGCACGTGCTGGCTAGCTGGTCTCAGCTGCACCCAGCCATGGGACCCTGGAGTCTGGACTCTATTGTACGCAGAGCCCCAGCTCCGGTGGGACTCACTCCGGATGATCAGTTTCTCTGTTTTCTTTTACTTTTGCCTTTTTTGTTTTTGAAAGAGTCTCACTCTTTAGCCCAACTTATCCTTGAATTCTTGGCAATCCTCCTGCCTCAGCTTACAAACATGAGTTACCACTGGTGGTGGTGAATCATGCCTTTCATCCCAGCACTCAGGAGGTAGAGATGGGTAGATCTCTGAGTTTGAGGCCAGCCTGGTCTAAAGAGTAAATTCCAGGACAGCCAGGGCTACAGAGAGAAACCTTGTCTCCAAAACAAAACCAAAAAAACAAAAACAAAACAAAGAAAAAACAAAAACAAAACAAAGAAAAAACAAAAAGAAAACAACAAAAACAACACAACAAAACCGCGTGAGCTACCAAGAATGGCCTATTTTGAGTTGTTGATTTTTGGTTGGTGGTTGGTTGTTTTTTTTCATCTACTGGACATCTTGAATGGATAGTTTAACCAAAATATAGTCAGTCATATCTACAGATTGTATCTACTTCTTGATTGTGGCTTTCATTGAACAACCAGCCATGGATGCTAAGGTTCATGCCATGCCTGCATCTACGACACCCTCCCCCAACATCAGGACCAGTCCCTTCAGTCACCCTGAAGGCAGAGCACCCTCCCCAGGGTCTATGTGACAGATATTCCTGTTATTGACTTAGCAAACAAGCAGGGACCAAACAGGGATGGAGGATGTGGCTTGGTCCAGCATGCACGATGCCCTGAACTTTATCTGCAGCACTGACCAAGCTGGGCACAGGAGCCCACCTGTGAGCCTAGCCCCCGGGAAGTGAAGGTAGAAGGCAGGAGGGGAAGAGTTCAAGGTCAACCTAAGCCACGTATAGAGTCATGTAGAGTTGGAGACTGGCCTGGGCAACAGGAAAGACTGTTAAACCCAGGAGTGCTGTTGCGTGCATTTGATCCAAGCTGCTGGAGACCCTAAGAGAGGAGCAATTATTTGAGTCTAGGACTTCAACACCAACTAGGGCAACATAGTGAGTTTCTGCCTTGAAAGTATGTAATTAGCACAGTTGGCCGTAGTGCCTGGGTGTTTCGGGCATGTGACCTCTAACACACTTCATCTCCTGCTCTCTCTGCAG
Seq C2 exon
CACACTGCAGCCGGGGATGAAGGCGGTGGCCAGTCACTGGTGTCGCCGGGCAGCTGTCTAGAGGACTTCCGTGCAACGCCATTTATCGAGTGTAACGGGGGCCGTGGTACCTGCCACTACTTCGCTAACAAGTACAGCTTCTGGCTGACCACGATCCCAGAGCAGAACTTCCAGAGCACACCATCCGCTGACACGCTCAAGGCTGGCCTCATCCGCACGCACATCAGCCGCTGCCAAGTGTGCATGAAGAATCTGTGAGGCTCCCGCCCTGCCCACGGCAGCTGTGTGGGAAGGCCACGTTGGTGCTTATCCTTCTGTATTTGTTTCAACTTTGTTTGAGACAATGTCTCACTTTTCATCCCTGCCTAGCCTGGAACTATGTAACCCCGGGCTGGCCTCCAACTTGTGGCAAACCTCCTGCCTCAGCTTCCCAGATGCTGGGATTATGGGCATGCGCCACCACACCCAGCTTGGTGCTTACTCTTAACTTATTACCTCAGATGCTGATCCCAAAGTTGATCTTAGTGTTTTCAAACTACCAAAGCAATTCTGCACCAGCACTCATTCCAACCGTCTGTCAGCAAGTGGGCACTAGCTCCTCCGGGATCTACCAGCCTTGGCTCACAGCCCTGCTAACACCCACCTTGGAGAGCCAACACCTAGGAGCAACCCACGGACCTCTCCCCATGTAGGACATAAACATCATGCTACCAGGTGTCCCCAACAATAGCTGTCTCTGTGTCCCTGTGCTTCCCCTGGCAACAGGCTGCTCACCTTCCTGCAGTCTTCCTAAAATGAGGCAGAGTCTAGGGGACAGCAAAGGAATCTATGGCCAATGATAGCTGAGCTCACTGACCCATTTCCACCCAAGGATGCATGCAGTGTGCTTCTGTCTAGACCTGGTTTCTTGGAGGAGGAGATGATAGCACTTTTTTCTATCAAATCCATAACTGCCACCTCCCAAGTCCCTACGTGTTGGCCCCTGCCTTTTTAAGACCCTGACGGCAGCTGGCACACAGCTCATGGCTCTAGCCAAACCCACAGCAAAGGAGACATCTCTCTAGCCCTCACCAGCATCTGCTGGAAGGTACACTTAGCAAATCATTGACAGTGGCGTCCTACAACCTGTGTCACCCTAAACACCTCCCTCCACAACCTGTTCCCTGCGGCAAGCTGTTCTATGGCTTTTCTGTGTAACACCATAAATAAAAGATATTCTAAGGACTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031503-Col4a2:NM_009932:47
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(26.1=31.2)

							
A:
NA

							
C2:
PF0141314=C4=PD(72.2=96.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000033899





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr13:110508222-110511933 
LOW PSI
HsaINT0039007
(COL4A2)
Human
(hg19)
chr13:111160569-111164280 
LOW PSI
HsaINT0039007
(COL4A2)
Rat
(rn6)
chr16:83387622-83389399 
LOW PSI
RnoINT0039790
(Col4a2)
Cow
(bosTau6)
chr12:89163465-89164989 
LOW PSI
BtaINT0041732
(COL4A2)
Chicken
(galGal4)
chr1:138384488-138387728 
LOW PSI
GgaINT0105271
(COL4A2)
Chicken
(galGal3)
chr1:143303029-143306269 
LOW PSI
GgaINT0105271
(COL4A2)
Zebrafish
(danRer10)
chr9:8899688-8904316 
LOW PSI
DreINT0049681
(col4a2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTTCAGCACCATGCCTTTCCT

				
R: 
CTCGATAAATGGCGTTGCACG

				
Band lengths: 
352-2164

			

		

	





	
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"