Special

MmuINT0119252 @ mm9

Intron Retention

Gene
ENSMUSG00000079484 | Phyhd1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:MGI Symbol;Acc:MGI:3612860]
Coordinates
chr2:30122383-30125367:+
Coord C1 exon
chr2:30122383-30122461
Coord A exon
chr2:30122462-30125208
Coord C2 exon
chr2:30125209-30125367
Length
2747 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGG
5' ss Score
8.76
3' ss Seq
GAGTCTTGTCCCTGCTGCAGTTC
3' ss Score
4.94
Exon sequences
Seq C1 exon
CCCTGGAGCCATCGAGCTGAGCCAGCTGAGTCCTGCAGTATTCCCCATGGCCTGCCTGAGTCCCTCACAACTCAAGAAG
Seq A exon
GTAGGGGCCCGTGGTTTGGAGGGTGCAGACCTCTAGTGACCTTTGAACTACCTCTGACATTTCACAAAGGAGAGAAAGATCCCTGCATATCAACCCTAATTTCTGCGAACAAAGCCCAAGAGGGCCAGGTCACAACACCACCTCCCCAGGTGCCATCTCCCCGGTCAGATACAGTGGGGGTTGGGGCTAGGAGGTAGAGAAACCACAATTCAGATTATCTAATCCAGCTAGCCCCAGGGGCCTGTTGATGAAGGCCTGGATAGGGCAGGCCAGTAGCTAGGTCAGCTCATTATGAAAGCCTACCATACAGGGGGTGGACTACGCACACTTTAAGTTAACCACCCCCAATCTCATATGCCAGGACTGTTAATGTATTAGATCTAGCCGAGGATCTTTGTTTCAAAGTCCCTCCTGGAGCTGTGGTTGGGGCTTAGCAGTTGAGTGCTTGCTTTAGGCTCCAAGATTTGATCCCAACACTCACAACACATACAGAAACACACACCACCACCACACACACCCCACACACACACACATACCACACACACCATATGCATACCACATACACATCAAAACACATACACAAACACATCACACATATCACCACACATAAACACGGCACACTCCACAATACATAAACACACACATACAAACAGACTACACACACACCAACACACATACATATACCACTATTACCACCACCACACACACCACACATCATGCATACACAGACACTCACACCACACACACACACACCATACTCACACACACATCCCATACAAATGCACACACACATACCGCACACACTCACATACAAACACATACATATGCATGCACACACCACACACACACACTCACACACAAATGCACCCATGTGCACATACACACAGAGACACATACATAAAAGCACACACATACCACACAGACAAACACTCATCACCCAACCCACACGCACTCACACAGACCTACTCTCTTTTGACAGCTGCCACTGCTGCCACAGTTCCCAAATTTGTCTGTGACTAAATATGTAGTGGAAGTCTGTCTGTCTTTTCCTTCTGTCTCACAGGCTATCTTTTGAGGGACAAAGCCCCATGTCAGTATTTTTTTGTACAGTTTGTGCTGAACTTTTGTTCAGTTTTTATGATTTCAAGCATGGAGGGCCTCCCTGTGTTAACCCTGAGTGATGGTTTGTTGCTCTGGCCTAGAACTCAGTCTGTAGAGCAGACTGCCCTTCAGCTCACAGAGCTCTGTCTGCCTCTGCTTCCTAAGTGCTGGGGTTAAAGGCATGGGCCACCATGCCTGGCCACGCTTACATCCTTGCTTTCTGTCCCTTACTGTGTTGGTTCTGTTTGTTTTCAGTGCTGGGAACAGGAGCCAGTCCTTGTACATGCTAGCAAGCAGTCAGCTTCTGAGAGGCGACCCAGTCACACACGTAATGTGCCTCAGCACCTTAGGCTAGCCTCAGAATAAAGAGACTTGGGGCAAAGTCAGAATCAGGCATCTGTGTTCACAGCCCCTAGCCTTCCCCACACTCACTCAGGAGAAAGAAAGCCAGCAAGGTCCTGCGACTGGGGACTTTCTAGCCTTGTCCTTCCTAGTGCTGGTGCTGACTCAAGCGTCCTGGCAGTCCCCTGCCGGCCCACACTGAGTAACACAATGGAAATAAAATTTCCAATGCATGGGTTTGGGGTTACAGGACAAGCCATAGCATGGGCAAATTCACTCTCCCTTCTGTCTGCTCCCCTGGCTATCCTCCCCTCACCCTGTGCTCCAGCCCTTCCCAATTTCCCAGTCGTCCAGTGCCCACAGGCTTTGTACTTCCTGTTCTCTGTCTTTAATGCTCTTTCCTATCTCTTTGCTTCCCAATGTTCTGCTCTTCCTTTAACCCCACTTCCTCCAAGCTGCCCATTGACCCCTTCACCTCGTAGATTCTTTGCCTTTAATTCTCAAAACCCTGCCCTTGTCTCCCTGTAAGTCAGTGTGATGTGGGATGGTATGTTTGTCTGATGGTAAGGGATGCATGGGTCTCCTTCACTGGACTATAAATTGTGTGAGTGTGGAGGGTGGCTGGTTCATAATCACATGTCCATCTGCTGAAGCTGTCTCGTACTCGCAATGCTTAGTCGGGATTGGAATAGCCTCCAAAGCCAGCATTAGAAGGCTGAGGCAGGAGGATCTTGAGTTTGAGGCCTCCCTGTCTTCAAACAAATAAAAACAAAACAAGGGAGTTAGGCGGGGTCGGTGGTTAAGAGTGCTTCTGCAAGCATGAAGATCAGAGTTCAAATCTCAGCACCCACTCCATGAGCTGCACACACCTGCAGCTCAGATCGCCAGGGCTCACAGGCTGCCAGTCTAATGAAGAAAACAGCCTAGGTTCAAGGAGAGCCTCAGAAATAGAAAGTGGAAGAGGGGCACCGTATGTCCTCTCCTGATGCCCCTGCACATGCGCACCTGCAGTTCTCACACATGTTCTACACTCACACCTGCACTTTAACACACAAATGAGCAAATGTTTCCGTATGTCCCAAACCCATTGGAGGGCAAGAGCAGAGGCAGCTGCCACTTCCCCTTCCTCGATAAGATGCAAGCAGCCAGTACTGACGGCTCCTCACTAAGCACTGGATGCCCATGTCCAGGGTGGGGGGCAGAGCCATGAGCAGGACACTTGATCTTGGTTCGAGTTTGTGGTCCAACATGGATATAAGGAATGAGCGAGGGCGGAAGGAGCCTGAGTCTTGTCCCTGCTGCAG
Seq C2 exon
TTCCAGGAGGACGGGTTTCTGCTGTTGGAAGGATTCTTCACAGCGGATGAGTGTGTGGCCATGCAGCAGAGGATCGGTGAGATTGTAGCTGAGATGGATGTCCCTCTGCACTGCCGGACAGAATTTTCCACCCAGGAAGATGAGCAACTTCAAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079484-Phyhd1:NM_172267:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.018 A=NA C2=0.089
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF057218=PhyH=PU(21.0=98.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000088663





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000099924, ENSMUSP00000109273, ENSMUSP00000109275, ENSMUSP00000116062, ENSMUSP00000116450, ENSMUSP00000119543, ENSMUSP00000121371, ENSMUSP00000121995
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:128922357-128927037 
ALTERNATIVE
HsaINT0124459
(PHYHD1)
Human
(hg19)
chr9:131684636-131689316 
ALTERNATIVE
HsaINT0124459
(PHYHD1)
Rat
(rn6)
chr3:8832814-8835804 
LOW PSI
RnoINT0110766
(Phyhd1)
Cow
(bosTau6)
chr11:99441701-99448980 
LOW PSI
BtaINT0111155
(PHYHD1)
Chicken
(galGal4)
chr17:5394180-5394932 
ALTERNATIVE
GgaINT1021466
(PHYHD1)
Chicken
(galGal3)
chr17:5949047-5949799 
GgaINT0126416
(PHYHD1)
Zebrafish
(danRer10)
chr21:4345218-4347308 
LOW PSI
DreINT0113728
(phyhd1)
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"