RetrogeneDB ID:

retro_pcap_163

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_127051:776..1388(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL13A
Ensembl ID:ENSPCAG00000004086
Aliases:None
Description:ribosomal protein L13a [Source:HGNC Symbol;Acc:10304]


Retrocopy-Parental alignment summary:






>retro_pcap_163
GCGAAGGAGCATGTGCTGGTGCCCGATGGCCGAGGCCATCTCCCGGGCTGCCTGGCAGCCACTGTGGCCCGGCAGGTGCT
GTTGGGCAGGAAAGTGGTGGTTGTGTGCTGTGAGGGCATCAACATTTTTAGCCACTTCTACAGAAACAAGTTGAAGTACC
TGGCTTTCCTCCACAAGCACATGAACACCAACCCATCCACGGTCCCTATCACTCCTGGGCCCCCAGCCGCACCTTCTGGC
TGACTGTGCGAGGCATGCCTGCCCCACAAGACCAAGCGTGGCCAGGCTACCTTGGACCACCTCAAAGTCTTTGATGGAAT
TCCAGCCTCCTGTGACAAGACAAAGCAGCTGGTGGTTCCCACTGCTGTCACAGCTGTGCGTCTCAGGCCCACACGGTAGC
TCACCTACCTAGGATGCCTAGCTCATGATGTACGCTGGAAGATTACCAGGCAGTGGCAGCCACCCTGGAGGAGAAGAGGA
AGGAGAAGGCCAACCAAGCTCCACCACAGAAAAAAGAAGCTGCTTATGAGGCTGAGGAAACCAGCCAAAAAGAACTTCTA
GAAAAGAAATGGCAGATACACAGAGGTTCTCAAGACCTACGGGCTCCTGGTC

ORF - retro_pcap_163 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.62 %
Parental protein coverage: 99.51 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalAEGQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPS-RGP
A...VLV.DGRGHL.G.LAA.VA.QVLLGRKVVVV.CEGINI...FYRNKLKYLAFL.K.MNTNPS..GP
RetrocopyAKEHVLVPDGRGHLPGCLAATVARQVLLGRKVVVVCCEGINIFSHFYRNKLKYLAFLHKHMNTNPS<HGP
ParentalYHFRAPSRIFWRTVRGM-LPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLG
YH..APSR.FW.TVRGM.LPHKTKRGQA.LD.LKVFDGIP...DK.K..VVP.A...VRL.PTR...YLG
RetrocopyYHSWAPSRTFWLTVRGM>LPHKTKRGQATLDHLKVFDGIPASCDKTKQLVVPTAVTAVRLRPTR*LTYLG
ParentalRLAHEVGWKYQAVTATLEEKRKEKAKLHYRKKKQLMRLR--KQAEKNLEKKIDKYTEVLKTYGLLV
.LAH.V.WK...........R...........K.....R..K.A.KN..K....YTEVLKTYGLLV
RetrocopyCLAHDVRWKITRQWQPPWRRRGRRRPTKLHHRKKKLLMRLRKPAKKNF*KRNGRYTEVLKTYGLLV

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






RNA-Seq - click to see more details

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Procavia capensis was not studied using ChIP-Seq data.

EST - click to see more details

Procavia capensis was not studied using EST data.

TSS - click to see more details

Procavia capensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_pcap_163 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 17 parental genes, and 97 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000052963 retrocopies
retro_btau_1251, retro_btau_719, retro_btau_789,
Canis familiaris ENSCAFG000000298923 retrocopies
retro_cfam_1772, retro_cfam_924, retro_cfam_976,
Callithrix jacchus ENSCJAG0000000007216 retrocopies
retro_cjac_1130, retro_cjac_1706, retro_cjac_182, retro_cjac_197, retro_cjac_1997, retro_cjac_2170, retro_cjac_2322, retro_cjac_2467, retro_cjac_2468, retro_cjac_2665, retro_cjac_2699, retro_cjac_2755, retro_cjac_3009, retro_cjac_664, retro_cjac_941, retro_cjac_972,
Echinops telfairi ENSETEG000000170762 retrocopies
retro_etel_46, retro_etel_853,
Gorilla gorilla ENSGGOG0000000293211 retrocopies
retro_ggor_12, retro_ggor_1739, retro_ggor_214, retro_ggor_2271, retro_ggor_2737, retro_ggor_334, retro_ggor_6, retro_ggor_615, retro_ggor_627, retro_ggor_846, retro_ggor_869,
Loxodonta africana ENSLAFG000000162133 retrocopies
retro_lafr_1160, retro_lafr_576, retro_lafr_810,
Macaca mulatta ENSMMUG0000000755114 retrocopies
retro_mmul_1100, retro_mmul_1256, retro_mmul_1638, retro_mmul_1756, retro_mmul_2179, retro_mmul_2249, retro_mmul_2352, retro_mmul_2399, retro_mmul_296, retro_mmul_500, retro_mmul_520, retro_mmul_547, retro_mmul_837, retro_mmul_924,
Mustela putorius furoENSMPUG000000026043 retrocopies
retro_mputfur_1418, retro_mputfur_853, retro_mputfur_935,
Mus musculus ENSMUSG000000741293 retrocopies
retro_mmus_1129, retro_mmus_1334, retro_mmus_20,
Oryctolagus cuniculus ENSOCUG000000252589 retrocopies
retro_ocun_1038, retro_ocun_1077, retro_ocun_1392, retro_ocun_1462, retro_ocun_304, retro_ocun_674, retro_ocun_756, retro_ocun_786, retro_ocun_972,
Otolemur garnettii ENSOGAG000000046257 retrocopies
retro_ogar_1496, retro_ogar_211, retro_ogar_2254, retro_ogar_3148, retro_ogar_54, retro_ogar_596, retro_ogar_612,
Procavia capensis ENSPCAG00000004086 4 retrocopies
retro_pcap_163 , retro_pcap_290, retro_pcap_415, retro_pcap_416,
Pongo abelii ENSPPYG000000102511 retrocopy
retro_pabe_148,
Pan troglodytes ENSPTRG000000112981 retrocopy
retro_ptro_31,
Pteropus vampyrus ENSPVAG000000109583 retrocopies
retro_pvam_129, retro_pvam_625, retro_pvam_771,
Rattus norvegicus ENSRNOG0000002061810 retrocopies
retro_rnor_1073, retro_rnor_1112, retro_rnor_1212, retro_rnor_1292, retro_rnor_1357, retro_rnor_1742, retro_rnor_564, retro_rnor_593, retro_rnor_665, retro_rnor_988,
Sus scrofa ENSSSCG000000031664 retrocopies
retro_sscr_290, retro_sscr_300, retro_sscr_392, retro_sscr_743,


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