Special

MmuINT0032023 @ mm9

Intron Retention

Gene
ENSMUSG00000025461 | Cd163l1
Description
CD163 molecule-like 1 [Source:MGI Symbol;Acc:MGI:2443796]
Coordinates
chr7:147410609-147414073:+
Coord C1 exon
chr7:147410609-147410923
Coord A exon
chr7:147410924-147413755
Coord C2 exon
chr7:147413756-147414073
Length
2832 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
TCCCTCTGCCTTTTCTACAGAAT
3' ss Score
9.88
Exon sequences
Seq C1 exon
GGAGCCTGCGCGTGAGGCTGGCTGCGGGCCCAGGTCGATGTGCTGGGCGTGTGGAGTTATTCTATCAGGGCTCCTGGGGCACTGTGTGTGATGATGCCTGGGACCTACAGGATGCACAAGTGGTCTGTAGGCAGCTGGACTGTGGCCACGCCCTCAGTGCTCCCCGGAATGCTCACTTTGGGGCGGGGACTGGGCACATCTGGATGGATGAGCTGCACTGCTTGGGAAATGAGTCTTCGTTGTGGAAGTGCCAGTCAGGAAGCTGGGGCCAACATGACTGCAGACACAAGGAGGATGCTGGAGTGTTCTGCTCAG
Seq A exon
GTGGGTGCCACCTCTGGACTAGCAGCGGAGTATCAAAAGCATGGCTTAGCGTCCATGGTTACCTTTCTAGCTCAAGAGAGAACTCTTCCTGCATTCCTACTCTGTGTAAACACACACACACACACACACACACACACACACACACACACACACACACACACACACACATCCTTCGTGTTACTTGTCTCTCCTTCCTCTCTCTCCCTATGTATTAATCCTTTCCCTCTCCTTAATTAAGCTCCCCTCTCCCCAACCCCACTTCACAAACCCATGTCCTACCCATCTCTAGAAGAGTTCTCCCTGCCCCCACAATCCCCTTTCTACCCTCCTGGCTTTTGGTTACTTCAGGTTATATATTCTAATCTAAAGATTTGGAGCTGTGATCCATAAAGAAAGAACATGTGACCTTTGCCTTTCTGGGTTTGAGTTTCACTCAGCAAAGCATTTCCAGTTCCGGTCATTGATTTCATTATTTCATTTTCCTTTACAGCTGATAGAATCCACAGTGCATATGCAATGAGCTTTCAGTATCCACAGCCAGCTGAAGGACACCTAATCAGGGTGGAGGATTCTCAAGATGCTAAACATGTATCTATCATATGAGTTAGCAATACTATTCCTTGGGTGTATACCCAAAGGAGCCAGTATTCTGCTACAGGGATACTTTTTTGGCAATGTTCACAGTTACTCCAACTATAATAGCTAGAAAATGAAAACAGCTGAGACAACTCCATTTTTTAAAAAGTATATGTCTTTCTTTGTCATCCTGGCTGTGTTGGAACTATCTGTGTAGACCAAGCTGGTCTTGAACTCACAAGAACCCTCTTGCCCTGCTTCTGCTTCCTGGGTGCTGGAATTAAAGTCATGTGCCACCATATCCAACAGATATCTCCAATTCTCAATTTTGATTTTGTCTTTTTTTTTGTTTTTTTGAGACAGGGTTTCTCTGTGTAGTCCTGGCTGTTCTGGAACTCACTTTGTAGATCAGGATGGCCTCGAACTCAGAAATCCACCTGCCTCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCATGTGCCACCACTGCCTGGCTTGATTTTGTCTTATTGTGTACTAGGAGCACAGTTTTTTTTTCTCTCTCCAGGACATCCTTGAGGCTATTGTGTTGATGGGATCATGTCTGGGGACATCATTCTTGAGTTTAGTATTTTGTTATTGTTCTCAGGAGAAGCACCAGGAATTTCTGGCTGTCATAGCGATTTTCCTGCTCTTTAGACTGTGAGATCTGTCTTTGTGCAAATGTGTATCTGCTCACCAATATTAACCTGTTAGCTCTCACTAAGAAAGCACAGGGATGAATAAGGGAAAGAAGGGAAAGAAATAGGCAAACAATCATAAGATATTAAAGAGACAGCCGGCGTGTAACATGCTTACTGATTAAAATGACCTTAAATTTATTAAATGACCTGTTTTAACTTTCCCAAGTTAGAGAAAGAATCTGAGCTGGACCTGGTGTTGCACGCCAGTAATCACAGCCACCAAGACAAGTACAGGCATCAACACAGACTGCATCCAAAAAAAAAAAAAAACAAAAACAAAAAAACCAAAAAAACCGTAAAAGACATTTCACTAAAGTGTTTACCTGGAACCAAGCCCACGATAGAACGTTCAACTGAAACATGTTGTCAAGAGAAACTTGTTTTTCAAGGATCCAATCTATAAAATTTGTAGGAAAGGCACGCATCTTCACCTTCTGACCATTATTTTATTTTATTTCTACGGACTTGACTTAAAACATACATAAGGGAGGTTGTGTAATATATTTGTGCCTAGCTTATTTCAGTTAACATCATTTCCTTCAGGATCACTTATGATGTTATGAATCACAGGATTTCCTTTTTCATTTTCATTGTATGAATATATGTGAGTGTCTTCATGCATGTATGTGCACCATGTATGTACCTTGGGGCCTGGGAGGCCCGCACTAGAGTTATCGGCAGTTGCGAGCCACCAAATGAGTCCTGGAAACTGAACCTTGGTTCCTTATGAGAGCAACAAAAGTCTTAATTTCTGAGCCATCTCTGCAGCCCCTAGCTATCCTTTTAGCAGGCTGGAAATATTCTTTTCTCTCCTAGTTTCTGTTTTGCATGTCTATATGTTATCCATATTTGAATCTACACAAAACATCTGTATTCATCTGTCACTGGACACAACTGTCATTTCCATGTCCTGGCTCTTGTCAATCATGCTGTAATCCAGAGCATGGATCTCTCCTTGAATCACAGATTTAACTTTCCTTGGTGGTGTTATAAGTCATATATATTTTTTAACCACTGTGACAAAATACTTAGAACATTTGAAAAGGAGGACAGAGTGATGTAGGTTCATGGTTTCAGAGCCTTCAGTAAATGGTTGGTTTCTGGGTAATGTTTAGGTAGAAGAAAGCAAAGACACTCACAGTGGCCAGAAAGCAACAGATATGGACAAGGGCCCACCCTCATTATCTACTTCATCAATTCAGGATCACCACTTAAAGTCTCTAGAATCTCCCCTAGTACTGCCACAACCTGGGAACAAAGCTCTCAATAATCTCGTTGGTGGCATTTATATTCAAACTGTAAGAGAACCCAGGGGTGGGACTGCTGGTTGTATGGCCCTACTTTTAGACTTCCAAGGAACCTCTGTTCTGCTTTCCACAGTTGCTGGAAACAAGAAAAACCCATGTGCAAGTGATGCCAGGGTATAACTGGGTCAAATGGCATTATCTGTCTGTGAGATTCTTGGGTTGGCCCGTTCCTTCTGAGCCTGTCAGAGGAGCCTGAAGGAGGGTCTCCCTCTGCCTTTTCTACAG
Seq C2 exon
AATCTGTGGCTCTGAGGCTTCGAGGTGGCACTAGTGGCTGCGTTGGATGGCTGGACGTGCTCTACAATGGGTCCTGGGGTGCTGTGTGCAGCAATGCACTCAGAGACATCTCCTTGAGCATCATCTGCAGACAGCTGGGATGTGGGGACCAGGGCTGGCTGGAGAACAGGCCTTCTTCTGGAGCTGGCCTGGGAATCTCCTGGGTGGATAATATCAAGTGTCGAAATCTACACAATGCCACCCTGTGGCAATGCCCTTCTGCCCCATGGAACCCGCACTCCTGCACCCAGGAGGAGGAGGTCTGGATTAACTGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025461-Cd163l1:NM_172909:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0053013=SRCR=WD(100=92.5)

							
A:
NA

							
C2:
PF0053013=SRCR=WD(100=92.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000026531





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000081497
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:7373641-7374441 
ALTERNATIVE
HsaINT0030819
(CD163L1)
Human
(hg19)
chr10:135273675-135278109 
ALTERNATIVE
HsaINT0094774
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr26:25716218-25717317 
BtaINT0002212
([1])
Chicken
(galGal4)
chr7:6903192-6903532 
GgaINT0045275
([2])
Chicken
(galGal3)
chr7:6871285-6871625 
GgaINT0045275
([3])
Zebrafish
(danRer10)
No conservation detected
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"