RetrogeneDB ID: retro_pcap_174

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_13695:18807..19466(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRIM1
• Ensembl ID: ENSPCAG00000007103
• Aliases: None
• Description: primase, DNA, polypeptide 1 (49kDa) [Source:HGNC Symbol;Acc:9369]

Sequence

>retro_pcap_174
ATGGAAAAGGAGATGCAGAAAATGAATCCATACAAGACTGGTACAGGTGTAATGTATTCCTGCAGACCCAGTCTGTTCAA
TAAGTGAAGCTGGGAACTTACCAGGCTCAGGAAAAAGAGCTGGTGTTTGACAATGATATAATGGACTACAACAATACGAG
ATGGTGTAGTTCTGCAGACATATATTCTAAGTGTTGTACCCTCATGACGATGGCCATATAAATCATCAACAGAGTTTTGA
AGGAGGATTTTGGACTTAAGTGTTGCCTCTGGGTATATTTTGGAAGGAGAGGTGTTCATTGTTGGGTTTGTGATGAATCG
GTTAGAAAACTGTCCTCAGCAGTGTGTTCTGGAATAGTCGAGTATTTGATTCTTGTAAAGGGTGGTCCAGACATTAAAAA
GAAAGTTGACCTCACTGAAAAAATCCACCCTTTTGTCAGAAGATCTATAAACATAATAATAAAATATTTTGAATAATATG
CCTTGGTTGGTCAAGATATTCTTGAAAATGAAAGCTGGGATAAGAATTTAGTCCTTGTTCCTGAAACAATGCATGATGAC
CTTCAATAAGGCTTCCAAAAGTGTCACAGTTCACTTCAGCGTTGGGAACATGTAAAGAAAGTAGCCAGTAGATATCAGAG
TAATGTGAACAATGACAAA

Alignment

ORF - retro_pcap_174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.34 %
• Parental protein coverage: 53.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LEKEMQKMNPCKIDIGAVYSHKPSQHNT-VKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADTCPKCWTL
          .EKEMQKMNP.K...G..YS..PS..N..VKLG..QAQEKELVFD.D..DY...R..CSSAD...KC.TL
Retrocopy MEKEMQKMNPYKTGTGVMYSCRPSLFNK<VKLGTYQAQEKELVFDNDIMDYNNTR-WCSSADIYSKCCTL

Parental  MTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGPDVKKKVHL
          MTMAI.II.R.LKEDFG.K..LWVY.GRRGVHCWVCDESVRKLSSAV.SGIVEYL.LVKGGPD.KKKV.L
Retrocopy MTMAI*IINRVLKEDFGLKCCLWVYFGRRGVHCWVCDESVRKLSSAVCSGIVEYLILVKGGPDIKKKVDL

Parental  SEKVHPFVRRSVNIITKYFEEYALVGQDILENKESWDKILALVPETMHDDLQKGFQKCQTSLQRWEYLKT
          .EK.HPFVRRS.NII.KYFE.YALVGQDILEN.ESWDK.L.LVPETMHDDLQ.GFQKC..SLQRWE..K.
Retrocopy TEKIHPFVRRSINIIIKYFE*YALVGQDILEN-ESWDKNLVLVPETMHDDLQ*GFQKCHSSLQRWEHVKK

Parental  VASKCQSNVKNDK
          VAS..QSNV.NDK
Retrocopy VASRYQSNVNNDK

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_174 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015297	1 retrocopy	retro_ecab_447,
Homo sapiens	ENSG00000198056	1 retrocopy	retro_hsap_339,
Mustela putorius furo	ENSMPUG00000001603	1 retrocopy	retro_mputfur_587,
Nomascus leucogenys	ENSNLEG00000017443	1 retrocopy	retro_nleu_1780,
Oryctolagus cuniculus	ENSOCUG00000003458	1 retrocopy	retro_ocun_1265,
Procavia capensis	ENSPCAG00000007103	1 retrocopy	retro_pcap_174 ,
Pongo abelii	ENSPPYG00000004672	1 retrocopy	retro_pabe_356,
Pan troglodytes	ENSPTRG00000022987	1 retrocopy	retro_ptro_271,
Pteropus vampyrus	ENSPVAG00000008017	2 retrocopies	retro_pvam_153, retro_pvam_703,
Sus scrofa	ENSSSCG00000000408	1 retrocopy	retro_sscr_499,
Tupaia belangeri	ENSTBEG00000012998	1 retrocopy	retro_tbel_2255,
Tursiops truncatus	ENSTTRG00000002153	1 retrocopy	retro_ttru_352,