Special

MmuINT0039949 @ mm9

Intron Retention

Gene
ENSMUSG00000031503 | Col4a2
Description
collagen, type IV, alpha 2 [Source:MGI Symbol;Acc:MGI:88455]
Coordinates
chr8:11434628-11437709:+
Coord C1 exon
chr8:11434628-11434771
Coord A exon
chr8:11434772-11437586
Coord C2 exon
chr8:11437587-11437709
Length
2815 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
GGAATTCTGTTCCCTTCCAGGAA
3' ss Score
9.14
Exon sequences
Seq C1 exon
GTGATCGAGGGTCGCCTGGAATGGACGGTTTCCAGGGCATGTTGGGACTTAAGGGAAGACAGGGCTTCCCAGGGACCAAAGGAGAAGCTGGATTTTTTGGAGTTCCTGGTTTGAAGGGCCTGCCTGGCGAGCCAGGGGTTAAAG
Seq A exon
GTATGTCCTTGCTTAAGATCCAGGGTTCTCCGTGTTTGGTAAATAAGCCAGACTTAGCAGGGGAAAATATCCAAATATCATATTTTCTCTCATATGGAGAATGAATATCCATAGGGACACGTGTGTGTATGCATGTGTGTGCATCTGTGTGCTTATGTGTGTGCATGCATGTGCACATATGCCATGAAAATACAAGGACAGGAATTGACGAGGAAGACAAACAGCCATGACCAAAGCGTGGCATGCGTGTGTCCTGATGAGTCCTGCAACCTTGTACAATACATGCTAATCAACAAACAAACGAGTCAGGTATGATGGTGACAACCATCACCCTGACTACTAAGGAGGAGCAGGCGAGAGGCTCCAAAGTTGAAGGCCTGGGTGGGATATATAGCAAACTCCAGGCCAGCCTGAAGAACTTAGTGAGACCATGTGTCAAAATGAAAATGTCTAAAAAACCATAAAAGGTGAAAGGTGTCACCTGCTAAAGGCCAGGAGCAGAGCATAGAGTCAGCGGGTGCGTCCCAGTGAGTGCAGGGCTGCAGGTCCACCTAGAAGCACCACACACATAACAACAACAAAAGGATGCTCCTCCCTCAGGGAACAGTGCTCCTCAGGGAACAGTGCTCCACCTTCAAGGCAGCCCTTGCTGCTTGGAGGGATCCTGGACCTCAGCATTCCAAAGCTGGAAGCTGCAAACACACAATCAGATGATCCCAGCTACAAGTCTCCTGCCATCTCCCCCACATACTGACAGTGGATCGTACAACCCTATCCAAAGCAAAATTAATGGGTCTGTTAAGAACTAAGATTGCCACAAAGCCCATTCCATCATAACTGGACCGTAGCAAGTGTGAGCTGCAGAGGCAAGAGCGGGGAGGAGTGTGCTTTGAAACAGAGGCATGGTGGTGCACAGCTTTAATCCCAGAGGCCGGGAAGCAGAAGCAGGTGGATCTACGCGAGTTCAAGGTCAACCTGGTCAACATAGTGAATTCAGGGACAGACAGAGTTACATAGTGAGACCCTACCTCAAAACAAAGAAATCAAACCACAAAGAGACACACAGACACACAGAGAAAGAAAGGCAGTGGGGTGGGGGGGCAGAGGACAGCTGGAGATGATTCCAGTCTCAATCCCTGGTGAATCTAAGGTTAGATTTGGTGATGGCCCCACAGCTAAGTACACTGAAAACCACCAGACTCCTCACCTTAAAACACTGAGCTGTAGCCCAGTGTAACGGGGTGAAGTGCAGCTCTTGGGAGACAGAGGCAGTCAAGTTTCTGTGACGTCAAGGCTAGCCTGGTACACATACTGAGTTCCAGGACAGCCAAAGCTATGTGGTGAGACCTTGACTCAGAAAAACAGATGAACAAATGAACGAAAGAACAAATGAATGACAAACAGTGAGTTGTGTGGTCCATAAATCTCACATCAACAAAGATGCTTAAAAAGAATGGATGGAAAAGAAACAGAGAAAAGGAAGCCTAGAGACAGGCTCTGTGTGAGTTGGGGACCCACCAGGGCTACAGAACAAGACCCTGCCTCAAAACACTGAGGAGAAAATAATCTTATGGGTTAGGGCTGGGACTATAGCTCAGTCACATGCATGCCAATCAGAGCTCAATCCCAGGCAAAGAAAGAAAGAAAAGAAAAAAAGTTCCCAAAATCCAAGCCTGGTCTTGAACTCCTGGGTTCAAACCTCCAACTTCATCCCCTCAGTAGCTGGAATAGCAGGCTGTCTTAGTCAGGCTTTCTATTCCTGCACAAGCATCATGACCAAGAAGCAAGTTGGGGAGGAAAGGGTTTATTCAGCTTACACTTCCACATTGCTGTTCACCACCAAAGGAAGTCAGGACTGGAACTCAAGCAAGTCAGGAAGCAGGAGCCGATGCAGAGGCCATGGAGGGATGTTACTTACTGGCTTGCTTCCCCTGGCTTGCTCAGCTTACTCGTATAGAACCCAGGACTACCAGCCCAGGGAGGCACCACCCACAATGGGCCCTCCCACCCTTGATCACTAATTGAGAAGATGCCTTACAGCTGGATCTCATGGAAACATTTCCTCAAGGGAGGCTCCTTTCTCTATGATAACTCCAGCCTGTGTCAAATTGACATACAAAACCAGCCAGAACACAGGCCTAATCCCACTGTGCCTAGCTAAAAGTTACAATTTTAACAGACTTGTAGCAAAATAGTTCTTCCAAGATTTTAACCCACACCTGTGTTCTTAAATAACTTTCATGCTAACGTAGATATTTCAGGCCATGGAGCAGAAGTTGATCTTTTACAATTTTAATTAGGAATAAGCATGGTGACGCGTGCCTGTAACCCCGGGACTTGGAAAGATCTGTGTGTGATGAGTTCCAGCAGTCTAGACTACGTGGAGTCTTATCTCAAAAGAAAACAGAACAAAAGGCTAAAAATTAGTATTAAATTAGGGGGCTAGAGAGATGGCTCAGAGGTTAAGAGCACCAACTGTTCTCTTCCAGAGGTCCTGAGTTCAATCCCCAGCAACCACAGGGTGGCTCACAACCATCTGTAATGGGATCCGATGTCCTCTTCTGGTGTGTCTGGAGATAGCTACAATGTACTCATATACATAAAACAAATAAATTAAATTAGGAATGCAGTTGCCCTGTGCTCTGAGGCCTTCTCTCCCTCAAGGTGACTCCTGCAGCCTCCCAGGGCTGTGATTCTCCTGAATGTTCATCCCTGAGAGCGACACCCGAAGCTCTGAGGACAAAACCAGTTTAGCATTTGATTCCCTCGCCATCCCTGGGGTCTCAGGACATGTCGGAATTCTGTTCCCTTCCAG
Seq C2 exon
GAAACCGAGGAGACCGGGGGCCCCCAGGACCACCTCCTCTCATCCTGCCGGGGATGAAGGACATCAAGGGAGAAAAGGGAGATGAAGGACCAATGGGCCTGAAAGGGTATCTGGGCTTAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031503-Col4a2:NM_009932:32
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=0.905
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0139113=Collagen=PD(26.7=40.8),PF0139113=Collagen=PU(77.4=98.0)

							
A:
NA

							
C2:
PF0139113=Collagen=PD(21.0=31.0),PF0139113=Collagen=PU(42.6=61.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000033899





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr13:110482660-110484904 
LOW PSI
HsaINT0038991
(COL4A2)
Human
(hg19)
chr13:111135007-111137251 
LOW PSI
HsaINT0038991
(COL4A2)
Rat
(rn6)
chr16:83397878-83400876 
LOW PSI
RnoINT0039775
(Col4a2)
Cow
(bosTau6)
chr12:89149065-89150600 
ALTERNATIVE
BtaINT0041715
(COL4A2)
Chicken
(galGal4)
chr1:138371254-138372098 
LOW PSI
GgaINT0105256
(COL4A2)
Chicken
(galGal3)
chr1:143289795-143290639 
LOW PSI
GgaINT0105256
(COL4A2)
Zebrafish
(danRer10)
chr7:50660925-50661112 
LOW PSI
DreINT0049881
(col4a6)
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"