Special

MmuINT0152229 @ mm9

Intron Retention

Gene
ENSMUSG00000029699 | Srcrb4d
Description
scavenger receptor cysteine rich domain containing, group B (4 domains) [Source:MGI Symbol;Acc:MGI:1924709]
Coordinates
chr5:136440489-136441755:-
Coord C1 exon
chr5:136441441-136441755
Coord A exon
chr5:136440567-136441440
Coord C2 exon
chr5:136440489-136440566
Length
874 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCCA
5' ss Score
3.75
3' ss Seq
TGTCTTCTCTCCTGCTCTAGTTC
3' ss Score
9.78
Exon sequences
Seq C1 exon
GTGAGGGCAGTGTGCGTCTGGTGGGCGGCGCCAGCCCGTGTCAAGGCCGAGTGGAGATTCTGCATGGTGGCGTCTGGGGCACTGTATGCGACGATGACTGGGGGCTGCAGGATGCTGCTGTTGTGTGCCGCCAGCTGGGCTGTGGGGTCGCCTTGGCCGCCACCACTAATGCCTTTTTCGGCTATGGTACCGGGCATATCCTGCTGGACAATGTTCACTGCGAAGGTGGCGAGCCCCGCCTGGCAGCCTGCCAGAGCCTAGGCTGGGGCGTGCACAACTGCGGACACCACGAGGATGCTGGGGTGCTCTGTGCAG
Seq A exon
GTGCCAGGGGCAGCGGGGGCGGTGCCAGGCTACGGGGCGGGGTCTTCGGAAGGAGTAAAGGTGGGAGGAGAACTGGAAGAAACTAATGGCTGAGTGGGAAAAGGGGTTGGCTATCTTTCCAGAAAGGCTTTGAAATTACCTGTACTATTCAGGCCCGCTCTGGGGAAGCAATTTGGATAACTCATTCGCACATTCTCAGTAGCTCTTATTCCTCCATTATTAGGACTGCTTCCAGAATTTTCTAGCAATTTCCAGGTATTCTTCATGGATGATTTCAGAATAAAGCAATAATATTCTAGAATGCTCCCTCAAAGATTACTTTCAAAGAACCTAACTGCAGAACCATGCCTAGCTATCTGTAACCCTGAGAATCTAATAATAGACTGCCCCCCCATATGGACCCTCTCCAATTTGGGAGGTGTTTTCAGCAAATTAAAGGTCAGCATTGGAGCAGAGTTATGTAGCTTATTTGATGGGGTGCTTTCCTAACATGCAAGAAGCCCTGGGTTTAATTTCCAGCCCCACACAAACCAGGCCTGCTGGTACATACTTACAGCTCTACTACTCCCTCAGCTACATAAAACCCTGAAGAAAAACAAAAACAAAAACAAGCCAGGCAGTGGTGGCACACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCAGATTTCTGAGTTCGAGGCCAGCCTGGTTAACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCAAAAAACCAAAATAAATAAATAAATAAATAAAGGACTGCTGTCAAAGCTGGCCAGGGCTCATTGAATGCCAGTCCTGGATGTAAAGCTGGTCCAATGACTGACCCTTCTGTCTTCTCTCCTGCTCTAG
Seq C2 exon
TTCTAAGCCCTCCGACTTCCACAGCTCTGCCTCCGTCTGTCACAAAAGAAGACTGGGCACGGCACACTGGGCCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029699-Srcrb4d:NM_001160366:6
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=0.701
 
                        

				
Domain overlap (PFAM):

					





						

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

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000106782





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000106783, ENSMUSP00000122958
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:76395331-76397517 
LOW PSI
HsaINT0158814
(SSC4D)
Human
(hg19)
chr7:76024648-76026834 
LOW PSI
HsaINT0158814
(SRCRB4D)
Rat
(rn6)
chr12:23757835-23759191 
ALTERNATIVE
RnoINT0143822
(Ssc4d)
Cow
(bosTau6)
chr25:34933275-34935997 
BtaINT0141314
(SSC4D)
Chicken
(galGal4)
chr19:4222532-4223234 
GgaINT1026428
(SSC4D)
Chicken
(galGal3)
chr19:4190688-4190825 
GgaINT0131333
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTGTCAAGGCCGAGTGGAGAT

				
R: 
TGCCGTGCCCAGTCTTCTTTT

				
Band lengths: 
342-1216

			

		

	





	
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






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