RetrogeneDB ID:

retro_pcap_334

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_39937:324..722(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS4X
Ensembl ID:ENSPCAG00000000761
Aliases:None
Description:ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]


Retrocopy-Parental alignment summary:






>retro_pcap_334
GCTCACGGTCCCAAAAAGCATCTAAAGCATGTAGCAGCTCAAAAGCACTTACATGATGGACAGAAAGACTGGTGTGCCTG
CTCCTTGTCCATCTGCCAGTCCTCAGCAAACTGAGAGAATGTGTCTCTCCCTGATCGTTTCCTTGAGAGATGTTTAAGTG
CGCCCAGTCAGAAAATGCATTAAAAGTCCGTATGCAGTGGTTATTAAGATTGATAACAGAAGCCTGGACTGATACTACTT
ATTCAGCTGATTTTATGGATGTCATCAACATCTACAGTGCCAGAGAGAGTTCCCGTCTGGTCCATGGCACCACAGGCCAA
TTTGCTGTTCATTGTATCACACCTGAGAATACAAAGCAGAAGTTATGCCAAGTAAGAAAGAACTTTGTGAGCACAGAA

ORF - retro_pcap_334 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 50.37 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalARGPKKHLKRVAAPKH-WMLDKLTGVFAPRPSTGPH-KLRECLPLIIFLRNRLKYALTGDEVKKICMQRF
A.GPKKHLK.VAA.KH..M.D..TGV.AP.PS..P..KLREC.....F.....K.A.......K..MQ..
RetrocopyAHGPKKHLKHVAAQKH>YMMDRKTGVPAPCPSASPQ>KLRECVSP*SFP*EMFKCAQS-ENALKVRMQWL
ParentalIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTK
........TD.TY.A.FMDVI.I....E..RL...T.G.FAVH.ITPE..K.KLC.VRK.FV.T.
RetrocopyLRLITEAWTDTTYSADFMDVINIYSARESSRLVHGTTGQFAVHCITPENTKQKLCQVRKNFVSTE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Procavia capensis was not studied using RNA-Seq expression data.
Procavia capensis was not studied using ChIP-Seq data.
Procavia capensis was not studied using EST data.
Procavia capensis was not studied using FANTOM5 data.
retro_pcap_334 was not experimentally validated.

Retrocopy orthology:
Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 23 parental genes, and 146 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146011 retrocopy
Ailuropoda melanoleuca ENSAMEG0000000580514 retrocopies
Bos taurus ENSBTAG000000188005 retrocopies
Canis familiaris ENSCAFG000000171512 retrocopies
Callithrix jacchus ENSCJAG000000041922 retrocopies
Cavia porcellus ENSCPOG000000063373 retrocopies
Equus caballus ENSECAG000000108526 retrocopies
Felis catus ENSFCAG0000001204111 retrocopies
Homo sapiens ENSG000001298241 retrocopy
Gorilla gorilla ENSGGOG0000002307918 retrocopies
Meleagris gallopavo ENSMGAG000000096711 retrocopy
Myotis lucifugus ENSMLUG000000116855 retrocopies
Macaca mulatta ENSMMUG000000032957 retrocopies
Monodelphis domestica ENSMODG000000110701 retrocopy
Mustela putorius furoENSMPUG0000000529411 retrocopies
Mus musculus ENSMUSG0000003132013 retrocopies
Otolemur garnettii ENSOGAG000000118082 retrocopies
Procavia capensis ENSPCAG00000000761 3 retrocopies
retro_pcap_334 , retro_pcap_35, retro_pcap_360,
Pongo abelii ENSPPYG0000002046224 retrocopies
Pan troglodytes ENSPTRG000000220259 retrocopies
Pan troglodytes ENSPTRG000000224701 retrocopy
Rattus norvegicus ENSRNOG000000032011 retrocopy
Sus scrofa ENSSSCG000000124055 retrocopies



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