RetrogeneDB ID: retro_pcap_318

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_34897:6404..6922(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK7
• Ensembl ID: ENSPCAG00000002566
• Aliases: None
• Description: cyclin-dependent kinase 7 [Source:HGNC Symbol;Acc:1778]

Sequence

>retro_pcap_318
ACATATCAGGTTGTAACCAGGTGGATTCAGGACCCTGAGTTACCTTCTGGAGCAAGGATATATAGAGTGGCCGTGGACAT
GTGGGCTAGTGGCTGTATATTAACAGAGTTGCTTCTAAAATTCCTTTTCTGCCAGGAGATTTGGACCTTGATCAGCTAAC
AAGAATATCTGAAACTTTGGTCACCCCAACAGAGGACCCATGGCTTGGTTTGTGTAGTCTTCCAGATTATGCAACATTTA
AGAGTTTCCCTGGAATCCCATTACAGCACATCTTCACTGTGGCAGGAGAGGACTTGCTACACCTTGTATAAGGCTTGTTC
TTATTTAATCCGTGCACTTGCATGACACTGAAAACTAAGTATTTTCGTAATAGGCCAGCCCTTACACCTGGGTGTCAGTG
GCCAAGACCAAACTGTCCAGTGGAGACTTTAAAAGAATAACCAGACTCTGCTGTGGCAACAAAACAGAGAAGAGCCAAGG
CCTTGGAACAAGGAGGATTATCCATGAAACTAATTTTT

Alignment

ORF - retro_pcap_318 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.03 %
• Parental protein coverage: 51.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  THQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLR-VPFLPGDSDLDQLTRIFETLGTPTEEQWP
          T.QVVTRW...PEL..GAR.Y.V.VDMWA.GCIL.ELLL...PFLPGD.DLDQLTRI.ETL.TPTE..W.
Retrocopy TYQVVTRWIQDPELPSGARIYRVAVDMWASGCILTELLLK<IPFLPGDLDLDQLTRISETLVTPTEDPWL

Parental  DMCSLPDYVTFKSFPGIPLQHIFIAAGDDLLDLIQGLFLFNPCTRITATQALKTKYFSNRPAPTPGCQLP
          ..CSLPDY.TFKSFPGIPLQHIF..AG.DLL.L..GLFLFNPCT..T....LKTKYF.NRPA.TPGCQ.P
Retrocopy GLCSLPDYATFKSFPGIPLQHIFTVAGEDLLHLV*GLFLFNPCTCMT----LKTKYFRNRPALTPGCQWP

Parental  RPNCPVETLKEQSNPAVATKRKRTEALEQGGLPKKLIF
          RPNCPVETLKE....AVATK..R..ALEQGGL..KLIF
Retrocopy RPNCPVETLKE*PDSAVATKQRRAKALEQGGLSMKLIF

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_318 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000134058	1 retrocopy	retro_hsap_2335,
Gorilla gorilla	ENSGGOG00000013349	1 retrocopy	retro_ggor_1772,
Mus musculus	ENSMUSG00000069089	1 retrocopy	retro_mmus_383,
Otolemur garnettii	ENSOGAG00000010748	1 retrocopy	retro_ogar_986,
Procavia capensis	ENSPCAG00000002566	1 retrocopy	retro_pcap_318 ,
Pongo abelii	ENSPPYG00000015525	1 retrocopy	retro_pabe_2114,
Pan troglodytes	ENSPTRG00000016946	1 retrocopy	retro_ptro_1707,
Tupaia belangeri	ENSTBEG00000012193	2 retrocopies	retro_tbel_587, retro_tbel_637,