RetrogeneDB ID: retro_pcap_341

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_42289:5822..6782(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000010626
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSPCAG00000015617
• Aliases: None
• Description: selenophosphate synthetase 1 [Source:HGNC Symbol;Acc:19685]

Sequence

>retro_pcap_341
CTCCCATCCCTGGGCATTGGGCTGGACTCGTGTGTTATACCGCTGAGGCACGGAGGTCTCTCCCTGGTACAGACTACGGA
CTTCTTTTACCCCCTGGTGGAAGATCCTTACATGATGGGGCGCATAGCTTGTGCCAACGTTTTGAGTGACCTTTACGCCA
TGGGCATCACTGAATGTGACAACATGCTGATGTTACTCAGTGTCAGCCAGAATATGCCTGAGGAGGAGCGAGAAAAGGTA
ACACCACTCATGATCAAAGGCTTTCGAGATGCTGCTGAGGAAGGAGGCACGGCAGTGACGGGCGGACAGACGGTGGTAAA
CCCGTGGATTATCTTAGGTGGGGTTGCCACCGTGGTGTGTCAGCCGAATGAGTTCATAATGCCCGACAGTGCCGTTGTTG
GGGATGTGCTTGTGCTGACCAAGCCCTTAGGAACCCAGGTTGCTGTCAACGCCCACCAGTGGCTGGATAATCCTGAAAGG
TGGAATAAAATAAAGATGGTGGTCTCCAGAGAAGAGGTCGAGCTGGCCTATCAGGAAGCGATGTTCAATATGGCTACCCT
AAACAGAACTGCTGCTGGACTAATGCACACCTTTAATGCCCATGCGGCCACAGATATCACTGGCTTTGGCATTCTAGGAC
ACTCTCAGAACCTTGCGAGACAGCAAAGAAATGAGGTGTCCTTTGTCATTCATAATTTGCCCATCATTGCCAAAATGGCC
GCCATCAGTAAGGCCAGTGGAAGATTTGGGCTTCTTCAAGGAACTTCAGCGGAAACCTCTGGAGGACTACTGATTTGTCT
GCCAAGAGAACAGGCGGCTCGCTTTTGTTCCGAAATCAAATCTTCCAAGTACGGAGAAGGTCATCAGGCGTGGATCGTCG
GCATTGTAGAAAAGGGAAACCGAACGGCCCGCATCATTGACAAGCCTCGAGTGATTGAGGTCCTACCTCGGGGAACCACT

Alignment

ORF - retro_pcap_341 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.93 %
• Parental protein coverage: 81.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGISN
          .P.LGIG.D.CVIPLRHGGLSLVQTTD..YP.V.DPYMMGRIACANVLSDLYAMG.TECDNMLMLL..S.
Retrocopy LPSLGIGLDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQ

Parental  KMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLT
          .M...ER.KV.PL.I.GF.DAAEE.GT.VTGGQTV.NPWI.LGGVAT.VCQPNEFIMPD.AV.GDVLVLT
Retrocopy NMPEEEREKVTPLMIKGFRDAAEEGGTAVTGGQTVVNPWIILGGVATVVCQPNEFIMPDSAVVGDVLVLT

Parental  KPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFG
          KPLGTQVAV..HQWLD.PE.WNKIK.VV..E.VELAYQEAM.NMA.LNRTAAGLMHTFNAHAATDITGFG
Retrocopy KPLGTQVAVNAHQWLDNPERWNKIKMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFG

Parental  ILGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEI
          ILGH.QNLA.QQRNEVSFVIHNLP..AKMAA.SKA.G..FGL..GT..ETSGGLLICLPREQAARFC.EI
Retrocopy ILGHSQNLARQQRNEVSFVIHNLPIIAKMAAISKASGR-FGLLQGTSAETSGGLLICLPREQAARFCSEI

Parental  KSPKYGEGHQAWIIGIVEKGNRTARIIDKPRIIEVAPQVAT
          KS.KYGEGHQAWI.GIVEKGNRTARIIDKPR.IEV.P...T
Retrocopy KSSKYGEGHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGTT

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_341 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 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013555	1 retrocopy	retro_amel_21,
Canis familiaris	ENSCAFG00000004743	2 retrocopies	retro_cfam_1787, retro_cfam_250,
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Loxodonta africana	ENSLAFG00000004670	1 retrocopy	retro_lafr_125,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Procavia capensis	ENSPCAG00000015617	1 retrocopy	retro_pcap_341 ,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,
Tursiops truncatus	ENSTTRG00000011114	1 retrocopy	retro_ttru_649,