RetrogeneDB ID: retro_pcap_143

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_10969:25603..26155(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NANOG
• Ensembl ID: ENSPCAG00000015460
• Aliases: None
• Description: Nanog homeobox [Source:HGNC Symbol;Acc:20857]

Sequence

>retro_pcap_143
TCTCCTCTTCCTTCCTTCATGGATCTGTTTATTCAACACAGCCTTGATTCTTCCACCACTCCCCAACCAAAACCACCTGC
TTCTGTAGAGAAGAGCAGGGTGAAGGTAGGGAAGGGCCAGGGCAAGAAGCAGAAGGTCAAAGGAGCATTCTCTCAGACCC
AGCTGTGCATACTCAAAGATAAATTTCAGAAACAGAAATACCTGAGCCTCCAACAGATGCAAGAACTTTCTGAAGTCCTG
ACCCTTAGCTACAAACAGGATGACATCTGATTCCAGAACCAGGGAATGAACTGTAAGAGTTGGCAGAAAAATACCAATGG
TGAAAGACCAGCTACGCTGTGACTCAAGTCTCAGCACCTACTGAATACCTGGACCTCTACACTCTGCTATTACCAGTGAT
GCTTCCCTTCTGGAAACCTTCCAACATGGAGCAACCAGGCCTGGAATGGTCAGTCTTGGAACAATCCTTGCTGGAACAGC
CAGGCTTGATGCACTGAAGCCTAGACTAATAAATCCTGGAATAACCAAGCCTGGAACCATCAGATGCAGAAC

Alignment

ORF - retro_pcap_143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.73 %
• Parental protein coverage: 77.97 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SPLPSSMDQLAQDSPDSSTSPKIKPLASASEKSLVKKEGKGQGKKQKVRTVFSQTQLCVLKDRFQKQKYL
          SPLPS.MD...Q.S.DSST.P..KP.AS..EKS.VK..GKGQGKKQKV...FSQTQLC.LKD.FQKQKYL
Retrocopy SPLPSFMDLFIQHSLDSSTTPQPKPPASV-EKSRVKV-GKGQGKKQKVKGAFSQTQLCILKDKFQKQKYL

Parental  SLQQMQELSEVLNLSYKQVKTWFQNQRMKCKRWQKNTT-WSKNGSGFTQKILTPNKFLELCS-SYHQGCL
          SLQQMQELSEVL.LSYKQ....FQNQ.M.CK.WQKNT..W.K.....TQ....P...L.L....Y.Q.C.
Retrocopy SLQQMQELSEVLTLSYKQDDI*FQNQGMNCKSWQKNTN<W*KTSYAVTQ-VSAPTEYLDLYT>CYYQ*CF

Parental  ---NNQTWNNPVWSNQTWNNSAWSNQTWNTQAWGNHSWNSQAWCTQSWN
          ...N..TW.N..W..Q.WNN..W..Q...T.A..N.SWN.QAW..Q..N
Retrocopy PSGNLPTWSNQAWNGQSWNNPCWNSQA*CTEA*TNKSWNNQAWNHQMQN

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_143 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 23 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017064	1 retrocopy	retro_amel_354,
Canis familiaris	ENSCAFG00000013914	1 retrocopy	retro_cfam_724,
Choloepus hoffmanni	ENSCHOG00000000972	4 retrocopies	retro_chof_1267, retro_chof_264, retro_chof_794, retro_chof_987,
Callithrix jacchus	ENSCJAG00000018999	8 retrocopies	retro_cjac_1732, retro_cjac_2234, retro_cjac_2441, retro_cjac_402, retro_cjac_4153, retro_cjac_4177, retro_cjac_880, retro_cjac_989,
Cavia porcellus	ENSCPOG00000002621	1 retrocopy	retro_cpor_1132,
Echinops telfairi	ENSETEG00000004648	8 retrocopies	retro_etel_1155, retro_etel_1334, retro_etel_134, retro_etel_1434, retro_etel_1935, retro_etel_630, retro_etel_818, retro_etel_963,
Felis catus	ENSFCAG00000001621	1 retrocopy	retro_fcat_932,
Homo sapiens	ENSG00000111704	5 retrocopies	retro_hsap_1455, retro_hsap_1549, retro_hsap_3713, retro_hsap_4814, retro_hsap_722,
Gorilla gorilla	ENSGGOG00000028196	4 retrocopies	retro_ggor_1812, retro_ggor_2510, retro_ggor_3000, retro_ggor_608,
Macropus eugenii	ENSMEUG00000009949	2 retrocopies	retro_meug_266, retro_meug_940,
Microcebus murinus	ENSMICG00000002228	1 retrocopy	retro_mmur_575,
Myotis lucifugus	ENSMLUG00000029325	2 retrocopies	retro_mluc_1562, retro_mluc_2054,
Myotis lucifugus	ENSMLUG00000030580	1 retrocopy	retro_mluc_169,
Macaca mulatta	ENSMMUG00000032158	4 retrocopies	retro_mmul_1901, retro_mmul_2466, retro_mmul_964, retro_mmul_979,
Monodelphis domestica	ENSMODG00000017979	2 retrocopies	retro_mdom_1293, retro_mdom_1938,
Mustela putorius furo	ENSMPUG00000016731	5 retrocopies	retro_mputfur_1140, retro_mputfur_1553, retro_mputfur_261, retro_mputfur_553, retro_mputfur_691,
Nomascus leucogenys	ENSNLEG00000005359	3 retrocopies	retro_nleu_1086, retro_nleu_2189, retro_nleu_2340,
Oryctolagus cuniculus	ENSOCUG00000013783	1 retrocopy	retro_ocun_971,
Otolemur garnettii	ENSOGAG00000026339	1 retrocopy	retro_ogar_568,
Procavia capensis	ENSPCAG00000015460	2 retrocopies	retro_pcap_143 , retro_pcap_429,
Pongo abelii	ENSPPYG00000004233	5 retrocopies	retro_pabe_2157, retro_pabe_3142, retro_pabe_3440, retro_pabe_3742, retro_pabe_623,
Pan troglodytes	ENSPTRG00000029807	4 retrocopies	retro_ptro_1746, retro_ptro_2514, retro_ptro_3203, retro_ptro_990,
Pteropus vampyrus	ENSPVAG00000006989	1 retrocopy	retro_pvam_1251,