RetrogeneDB ID:

retro_pcap_319

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_3503:9095..9542(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS18
Ensembl ID:ENSPCAG00000005854
Aliases:None
Description:ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]


Retrocopy-Parental alignment summary:






>retro_pcap_319
GTGTCTCTAGTGATACCTGAGAAGTTTCAGCACATTTTGTGAATACTCAACACTGACCTTGATGTGCTGTGGAAAATAGC
CTCTGCCATCACTGCCATTAAGGGTACGGGGCAAAGACATGCTCATGTGGTGTAGAGGAAAACAGACATCGACCTCACCA
AAAGAGCAGGAGAGCTACCTGAGGTTGATGTGGAGCATGTGATCACCATTACGCAGAATCCATGCGAGTATAAGATTCCA
GACTGATTCTTGAACAGACAGAAGGACGTGAAGGATGGGAAATACAGTAAGGTCCTGGCCAATGATCTGGAAAACAAGAT
GCAAGAAGACGTGGAGCAGCTGAAGAAGATGTGGGCCCACAGAGGACTGCCCCACTTCTGGGGCCTTTGTGTTTGAAGCC
GCCACACCAAGATTACTAACCACCGTGGCTGCACTTTGGGTGTGTCC

ORF - retro_pcap_319 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.48 %
Parental protein coverage: 98.03 %
Number of stop codons detected: 4
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
.SLVIPEKFQHIL..LNT..D...KIA.AITAIKG.G.R.AHVV.RK.DIDLTKRAGEL.E..VE.VITI
RetrocopyVSLVIPEKFQHIL*ILNTDLDVLWKIASAITAIKGTGQRHAHVV*RKTDIDLTKRAGELPEVDVEHVITI
ParentalMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTG
.QNP..YKIPD.FLNRQKDVKDGKYS.VLAN.L.NK..ED.E.LKK..AHRGL.HFWGL.V...HTK.T.
RetrocopyTQNPCEYKIPD*FLNRQKDVKDGKYSKVLANDLENKMQEDVEQLKKMWAHRGLPHFWGLCV*SRHTKITN
ParentalRRGRTVGVS
.RG.T.GVS
RetrocopyHRGCTLGVS

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_319 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 14 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000009507 retrocopies
Dipodomys ordii ENSDORG000000138256 retrocopies
Gorilla gorilla ENSGGOG000000065715 retrocopies
Loxodonta africana ENSLAFG000000321731 retrocopy
Macaca mulatta ENSMMUG000000038671 retrocopy
Mus musculus ENSMUSG000000086682 retrocopies
Nomascus leucogenys ENSNLEG0000000684010 retrocopies
Oryctolagus cuniculus ENSOCUG000000105461 retrocopy
Procavia capensis ENSPCAG00000005854 2 retrocopies
retro_pcap_235, retro_pcap_319 ,
Pongo abelii ENSPPYG0000002595314 retrocopies
Pan troglodytes ENSPTRG000000180391 retrocopy
Rattus norvegicus ENSRNOG000000285054 retrocopies
Sarcophilus harrisii ENSSHAG000000068572 retrocopies
Sarcophilus harrisii ENSSHAG000000086581 retrocopy



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