Special

MmuINT0039916 @ mm9

Intron Retention

Gene
ENSMUSG00000031502 | Col4a1
Description
collagen, type IV, alpha 1 [Source:MGI Symbol;Acc:MGI:88454]
Coordinates
chr8:11202894-11206403:-
Coord C1 exon
chr8:11206226-11206403
Coord A exon
chr8:11203009-11206225
Coord C2 exon
chr8:11202894-11203008
Length
3217 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
GCCTGCTTCCTCTCTTCCAGGTG
3' ss Score
12.79
Exon sequences
Seq C1 exon
GTACGGCTGGCAGCTGCCTGCGTAAGTTCAGCACCATGCCCTTTCTCTTCTGCAACATCAACAACGTCTGCAACTTCGCCTCCAGGAACGACTACTCTTACTGGCTGTCCACGCCAGAGCCCATGCCCATGTCCATGGCACCCATCTCTGGGGACAACATCCGGCCCTTCATTAGCAG
Seq A exon
GTGAGCTTAGCATCCAGAGGCAGTTGTTAAAAATGAAGACGAGAAATCGGTGCACACTTGGCCTTGAATGTAGAGAGGTCTGCTTCTGCCTTCCCAGGACTGGGGTTAAAGGCATGCACCATCATGCTTTTTTTCTTTAAAAGAAGATTTGTGCATGTGTGCGTGCGTGCGTGCGTGCGTGCGTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTATGTGTGTGTGTATGTGCACATGTGCAGCTGTCCTTGTAGCCAGAGACATCAGATCCTCCTGGAGCTGGAGTTACATGGAGTTGAGAATCACCTGCTATGGGTGGTGCTGGGAGCCTCTTCTGGGTCCTTTGCATTTTCTTAGCCACACTAATTCATCTCTCCAGCTCCCAAATGTCCTTTCTTAAAGGGTGAATGGATGCACATTGGATTTTGTGTATCCACGGCTGTCTGGGTTGGCTGTTCTGACTAAGCCTACTCCGAATGCGGGTGCCTTCCGACCTTTTGCTCCATCCAGAATTGGGGTTGCTGAGTCACACGTTGATTCTATTTTTAAGCGTTTGAGTTTGAGACACTTCCTTACTGTTTTTCCCCCCAGTGGCCGTGCCCTTGATGCCCTTGACATCATGACATCCCCACCGGCCACGCACAAGGGCTCTCTCCCCCTTTGCCTTCACATCCTCACTAACACTTGTCAGTCTCTGTTGTGTTTTTCACAGTAGCCCAAGTGGTTGCAAAATGAAGCCCGTGGGACTGTAGTACCGAATATATAATACCTGTCTCATCTGCTTGTGTAGTGTTTGTGCATAAAAATTATTTCAGATTCATTTCACTCAGAAACTTAGGCGTGATCACTAGCACCCCAGAATTGATGGTGGAGGAGCACAGATCCATTTCCTGTCCCCTGTCCCATTGAAGTTTGCTCCCTTGAGACTGTGTAATACTGATTGAGAATGCGTATGTCTCTGGCTGAGTGATTCCCACATTAAGCTTGTCCCCACAGTGGCAGACATCTGGAGTGTTTTCAACTCAAGATCTTGCCTGGTAGGAAGTAAGGCTGGACATTTTATGAGTGAAAAGTATTAGATTGTCCTATTATTTTTTTTGCTTGCTAATTTCCTTCAAAATAAGTTTATTGTTCAGTTGTACTAAGAAGTGACAGAAACATGGAAATGGACAGACTCACTTGGCCAACGATTCACTTTGTGCGTGCAGTATATTAAAGACAGAGGAATGAGATCTCGGGAGCATCCCTTAGGGACTGACGAGAAAGCACCAGGCATCCTCATGTACTCTTGCGAGGCAGCGCTCACTATGCAGCCCAGGTTGGCCTTGAACTCGAGATCCTCATGCCTCAACCTCTTAAGTGATCGGATTTTGAGTCTGCTCCACCATGCCGAGATCTTCACAGGTCCTTTAAAAACAGGAGCGAGCATGAAGACAGACAGACAGACAGGCAGCCTGGCAGATCAGCTTTACCAGAGGGTCACAGACTTTCTGTGGCTGTGCTCTGAAGTCCCTCGTGACAGCCTTTTTCCTAAATGGAAAATGTCATTTATTACACTTGAAGAGTACACAGAGCATGCCGTACAGACGTGTGATCTGTATGCAGACCCCTGCCCAGGCTGTGTTGAAGGCACTAGAAGGAGAACTAACTTTCTGTGGTTTTTCTTTTTAGCTTTCCTTGGAAAACAGGTAGAAAATGTTTATTATTGATGTCTCTTGGTTACTTTTGGAATGGCGTCTATGCTGGTCTTGACTTGGTTGAAGACACAGGCCCAGGGAAACTGTGTGTCTCATTCTTTTCTCCATGGGCATTTGTCTTCACAAAGTTCCTGTTCTGTGAGCACACCTGAGATGTATACCTAAAATTTGGCATTTCAGGGTTCTTTATGTCCCTGCAGCTTGAGGGGCCCTTCAGGTCTCACCCAGCCACACAGGCATCTCTAATTCCCTGTTGTAGGGATGTGGCCTCCTCCCTGGGCTGAGAGTTACTTTAGCTTGATGGTTTCCAGCAATGTCTCAGGACTTCCAGGTCCCTTCTCTCCTGTGGGAAGACCCAAAAGCTTAATTTTAGAAACATTGACATAAATCTTTCCTTTTGAGTTTTGAGCCGAAGAGATGTCAGCTGCTTTCTTTATCCTGTTGGCTACAATTTCTAAGTACTTTCTACAGACAGGAGTGGCCATAAAGCCACAATTCCATCACCTGAGAGAAATGACCGGTGGTCAGAGCGGAAGGGAATTTGTGATGGCCTGGGCTGTGACACTAACCACAGCTGTCCTTCTCTTTGGCCTGCCCCTCCTCTCCCCCCTAGCACCAAAGCATCCTGGGAAGAAGGGCACTTTATTTCCCATGCCTGAAAGGCAGAAGGCAGCAGATGGACAAGGCCATTTCAATTTCAGTGGCTGGTGTTTAATGGAACCTTTTAGTTCATCTACATTTATGTGACTAAAGTAGAGAGAGTGTGTGTGCATGCATACACACACACACACAGACACATGCACACACAGACAGACAGAAGCACATACACATATGTGTGCATGTCCACACAGACAGACACACACAGAGACAGACAGACAGACAGACAGACACACACACACACACACACACATACGCACGCACGAATGCACAGCACAGAAAATGGAATGACTAATCTAGCCGCCCGCCCACCCACTTCCTGTCCACGCATGCAGAACTTGTGTAATTATTCACACGTTTGTACTCATTTAGCAGCGTGGCTAACACTCTCTTCACTCTGTGACTGGAATGTAATTATTTTGCTGCTGCTGTTTGTGTTTTTAAGCAGTGCACTCCCCCACCATCCAGTACTCCCTTACTTGAGTGAGCTTTAGAACACCCGACCACGCTGTGGTTTTCACTCACTCTGGGGTGACTTGTCATGGCTGGGCTTGAGCTAGCCTGTCCCAGGAGGGACTTTGTCCTCAGGAGGGGCCAGAACAGTGATTCCCTCTGCCACGGTTATGACGATCCCATTGTTCCTCTTATAGAATAGTTTAAAAAAAAATCAACTGCTTTTGAATTGAATGTTTTAGGAGTGAGACGGGCTTGTACAACCAAAGAGGAGTCCCTGAGCCTGAGTCCTGGCACTGGCCACATTATTTATTCACTTAGATTTGAGCCAGAGAACCAGGGAGAGAGGGCAAGGGATGGGTCATCCCCAGGACCATCCACACGGAATGCCTGCTTCCTCTCTTCCAG
Seq C2 exon
GTGTGCGGTTTGTGAAGCACCGGCCATGGTGATGGCGGTACACAGTCAGACCATTCAGATTCCGCAGTGCCCTAACGGTTGGTCCTCACTGTGGATCGGCTATTCCTTCGTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031502-Col4a1:NM_009931:49
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.033 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0141314=C4=FE(53.6=100)

							
A:
NA

							
C2:
PF0141314=C4=PD(6.4=17.9),PF0141314=C4=PU(26.3=76.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000033898





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000033898f6033A
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr13:110155398-110161191 
LOW PSI
HsaINT0038958
(COL4A1)
Human
(hg19)
chr13:110807745-110813538 
LOW PSI
HsaINT0038958
(COL4A1)
Rat
(rn6)
chr16:83624296-83627804 
ALTERNATIVE
RnoINT0039745
(Col4a1)
Cow
(bosTau6)
chr12:88879935-88883342 
ALTERNATIVE
BtaINT0041686
(COL4A1)
Chicken
(galGal4)
chr1:138141025-138144353 
LOW PSI
GgaINT0116576
(COL4A1)
Chicken
(galGal3)
chr1:143059045-143062373 
LOW PSI
GgaINT0116576
(Q9I9K3_CHICK)
Zebrafish
(danRer10)
chr9:8660763-8660990 
LOW PSI
DreINT0049660
(col4a1)
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






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