RetrogeneDB ID: retro_pcap_99

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_5989:86919..87561(-)
• Located in intron of: ENSPCAG00000009521

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ATP5C1
• Ensembl ID: ENSPCAG00000004971
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 [Source:HGNC Symbol;Acc:833]

Sequence

>retro_pcap_99
AAAGCTGCTATTGAGGCACCTGAGGGCAAGAAGAAACACCTCCTTGTTTGGTGTGTCATCAGATCGAGGACTTTGTGGTG
CTGTTCACTCCTCAGTTGCTAAGCAGATGAAAAGTGACGTGGCCCCCTCACGGCTGCTGGAAAAGAAGCTGTGATTGTTG
AAGTTGGTGATAAAATCAGGAGCATACTTCAGAGGACTCATTCTGACCAGTTTCTGGTGACATTCAAAGAGGTGGGAAGG
AAACTCCCTAGTTTTGGAGATGCATCAGTTATTGCCCGTGAATTACTAAATTCTGGATATGGATTTGATGAAGGATCTGT
CATCTTTAACCAATTCAGGCCTATCATCTTCTCTAAGACAGAAGAAAAGCCTTTATTTTCCCTCAGCACCATTGCGAGTG
CTGAGACTATGAGCATCTCGGATGATACTGATGCTGATGTGCGGCAAAATTACCAAGAATACAGTCTGACAAACCTCAAC
TGCTCTCTAAAGGAATCGACCACTAGTGAGCAGAGTGCAAGGATGACAGCTATGGACAGCACTAGCAAGGATGCTTCTGA
GATGACTGACAAACTGACTTTGACATTCAGTCGTACCCACCAAGCTGTCATCACGAAAGAATTGAGTGAAATCGTCTCTG
GA

Alignment

ORF - retro_pcap_99 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.65 %
• Parental protein coverage: 72.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KADIKAPEGKKKHLII-GVSSDRGLCGAIHSSVAKQMKSEVAT-LTAAGKEVMIVGVGDKIRGILQRTHS
          KA.I.APEGKKKHL...GVSSDRGLCGA.HSSVAKQMKS.VA..LTAAGKE..IV.VGDKIR.ILQRTHS
Retrocopy KAAIEAPEGKKKHLLV>GVSSDRGLCGAVHSSVAKQMKSDVAP<LTAAGKEAVIVEVGDKIRSILQRTHS

Parental  DQFLVTFKEVGRKPPTFGDASIIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFSLNTIASAETMS
          DQFLVTFKEVGRK.P.FGDAS.IA.ELLNSGY.FDEGS.IFN.FR..I..KTEEKP.FSL.TIASAETMS
Retrocopy DQFLVTFKEVGRKLPSFGDASVIARELLNSGYGFDEGSVIFNQFRPIIFSKTEEKPLFSLSTIASAETMS

Parental  IYDDIDADVLQNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTRQAVITKE
          I.DD.DADV.QNYQEYSL.N....SLKESTTSEQSARMTAMD..SK.ASEM.DKLTLTF.RT.QAVITKE
Retrocopy ISDDTDADVRQNYQEYSLTN-LNCSLKESTTSEQSARMTAMDSTSKDASEMTDKLTLTFSRTHQAVITKE

Parental  LIEIISG
          L.EI.SG
Retrocopy LSEIVSG

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_99 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005024	1 retrocopy	retro_cfam_1781,
Choloepus hoffmanni	ENSCHOG00000011229	3 retrocopies	retro_chof_102, retro_chof_297, retro_chof_673,
Callithrix jacchus	ENSCJAG00000020635	7 retrocopies	retro_cjac_1079, retro_cjac_1293, retro_cjac_1381, retro_cjac_1636, retro_cjac_2506, retro_cjac_4190, retro_cjac_526,
Cavia porcellus	ENSCPOG00000010523	2 retrocopies	retro_cpor_422, retro_cpor_984,
Echinops telfairi	ENSETEG00000010549	1 retrocopy	retro_etel_1406,
Felis catus	ENSFCAG00000000196	1 retrocopy	retro_fcat_818,
Homo sapiens	ENSG00000165629	1 retrocopy	retro_hsap_1415,
Gorilla gorilla	ENSGGOG00000009719	1 retrocopy	retro_ggor_1094,
Macaca mulatta	ENSMMUG00000009207	1 retrocopy	retro_mmul_2254,
Monodelphis domestica	ENSMODG00000016720	1 retrocopy	retro_mdom_1287,
Mus musculus	ENSMUSG00000025781	4 retrocopies	retro_mmus_1122, retro_mmus_2008, retro_mmus_3451, retro_mmus_3644,
Nomascus leucogenys	ENSNLEG00000011917	1 retrocopy	retro_nleu_1836,
Oryctolagus cuniculus	ENSOCUG00000004642	2 retrocopies	retro_ocun_1171, retro_ocun_363,
Otolemur garnettii	ENSOGAG00000015242	2 retrocopies	retro_ogar_1099, retro_ogar_2738,
Procavia capensis	ENSPCAG00000004971	1 retrocopy	retro_pcap_99 ,
Pongo abelii	ENSPPYG00000002076	1 retrocopy	retro_pabe_1170,
Pan troglodytes	ENSPTRG00000002277	1 retrocopy	retro_ptro_968,
Pteropus vampyrus	ENSPVAG00000006512	3 retrocopies	retro_pvam_1466, retro_pvam_51, retro_pvam_530,
Ictidomys tridecemlineatus	ENSSTOG00000026133	1 retrocopy	retro_itri_665,
Tupaia belangeri	ENSTBEG00000011530	4 retrocopies	retro_tbel_1763, retro_tbel_2023, retro_tbel_4384, retro_tbel_4406,
Tarsius syrichta	ENSTSYG00000003035	4 retrocopies	retro_tsyr_1268, retro_tsyr_1988, retro_tsyr_465, retro_tsyr_506,