RetrogeneDB ID:

retro_pcap_82

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:GeneScaffold_4689:305526..305970(+)
Located in intron of:ENSPCAG00000013586
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL23A
Ensembl ID:ENSPCAG00000017002
Aliases:None
Description:ribosomal protein L23a [Source:HGNC Symbol;Acc:10317]


Retrocopy-Parental alignment summary:






>retro_pcap_82
GCGCCTGCTCCTCCCAAAACTGAAGCCAAAGCCAAGGCATTGAAGGCTAAGAAGGCGGTGCTGAAAGGCGTCCACAGTCA
TAAAAAAAAGAAGATCCGTACTTCACCCACCTTCCGGCGGCCCAAGACACTGAGACTAAGGAGACAGCCCAAATATCCTT
GGAAGAGCGCCCCCAGGAGAAACAAGCTGGACCACTGTGCCATCATCAAGTTCCCTCTCACCACTGAGTCAGCCATGAAG
AAGACAGAAGATAACAACACACTTGTGTTCATTGTGGACATCAAGGCCAACAAGCACCAGATCAAACAGGATGTGAAGAA
GCTATATGACATTGATGTGGCCAAGGTCAACACCTTGATCAGACCTGATGGAGAGAAGAAAGCATATGTTCGTCTAGCTC
CTGACTATGATGCTCTGGATGTTGCCAACAAAATTGGAATCATC

ORF - retro_pcap_82 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.59 %
Parental protein coverage: 82.22 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAPAPPKTEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIK
APAPPKTEAKAKALKAKKAVLKGVHSH...KIRTSPTFRRPKTLRLRRQPKYP.KSAPRRNKLDH.AIIK
RetrocopyAPAPPKTEAKAKALKAKKAVLKGVHSHXXXKIRTSPTFRRPKTLRLRRQPKYPWKSAPRRNKLDHCAIIK
ParentalFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRLAPDYDALD
FPLTTESAMKK.EDNNTLVFIVD.KANKHQIKQ.VKKLYDIDVAKVNTLIRPDGEKKAYVRLAPDYDALD
RetrocopyFPLTTESAMKKTEDNNTLVFIVDIKANKHQIKQDVKKLYDIDVAKVNTLIRPDGEKKAYVRLAPDYDALD
ParentalVANKIGII
VANKIGII
RetrocopyVANKIGII

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_82 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 22 parental genes, and 446 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000468431 retrocopies
Bos taurus ENSBTAG000000463946 retrocopies
Callithrix jacchus ENSCJAG000000131267 retrocopies
Cavia porcellus ENSCPOG000000014526 retrocopies
Dasypus novemcinctus ENSDNOG0000001948765 retrocopies
Equus caballus ENSECAG000000089281 retrocopy
Felis catus ENSFCAG0000000402135 retrocopies
Gorilla gorilla ENSGGOG0000001673626 retrocopies
Loxodonta africana ENSLAFG0000001338716 retrocopies
Myotis lucifugus ENSMLUG000000124484 retrocopies
Monodelphis domestica ENSMODG000000192973 retrocopies
Mustela putorius furoENSMPUG0000001417912 retrocopies
Mus musculus ENSMUSG000000585468 retrocopies
Nomascus leucogenys ENSNLEG0000000287260 retrocopies
Procavia capensis ENSPCAG00000017002 30 retrocopies
Pongo abelii ENSPPYG0000000810849 retrocopies
Pteropus vampyrus ENSPVAG0000000292232 retrocopies
Rattus norvegicus ENSRNOG000000233446 retrocopies
Sarcophilus harrisii ENSSHAG0000001454913 retrocopies
Sus scrofa ENSSSCG000000177689 retrocopies
Sus scrofa ENSSSCG000000298024 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000001132823 retrocopies



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