RetrogeneDB ID: retro_pcap_176

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_1373:89240..90028(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB1
• Ensembl ID: ENSPCAG00000002451
• Aliases: None
• Description: cyclin B1 [Source:HGNC Symbol;Acc:1579]

Sequence

>retro_pcap_176
AAGACCAGTATGGCAGGTGCCAGGTGGGTGGCTGTGGCCACTGCTGCAGCCTCCAAGCCCAGGCTGAGGTCAAAAGTAGC
CCTTGGGGACACTGGTAACAAAGCCAGTGAACAGCCACAGGCTGAAATGTCTCTGAAAAAAGGAAACAAAAACTTCAGCT
GCTGGGACAAGTTATTGCCAAAAAAACTGCCAAAACCTCTGGAAAAGTCACCTTTGCCTAAGCCTGATCCCGAGCTACAA
TCTCAGCCTGCTGAAGAAGAAAAACTTTCACCTGAGCCTGTTTCTGTGGCTACTCCCTCACTGAGCCCATTGGAAACATC
TGGACGTGCCCAGTGAAAGAACATCTGTGTCAAGCTTTCTCTGATGTAATTCTTGCAGTGAGTGATGTGAATGCAGAAGA
TGGAGCTGATCCAAACCTTTTCAGTGAATATGTGAAAGACATCAACGCTTATCTAAGACAACTTGTGGAAGAGTAAGTTG
TCAGACTAAAATATCCAATGGGTGGAGAAGTCACTGAAAACATGATGGCAGTCCTAATTGACAGGCTAGTACAGGTTCAA
ATGAAATTCAGGTTGCTCCAGGAAACCACGTACATGACTGTTTCCGTTGTTGACCAGCTGATGCAGAATCATTGTGTTCC
CAAGAAGATGTCACACTGGGTTGCCGTCACCACTGTGTTTATTGCAAGCAAATATGAAGGAGTACACCCTCCAGAAGTTG
ATAACTTTGCCTTTGTGACTGACCACACTTAGACTAAGTACCAGATCAGCCAAATGGAAATGAAGATT

Alignment

ORF - retro_pcap_176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 62.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTSMAVPKRVPVATAAVSKPGLRPRVALGDIGNKVSEQPQAKMPLKKEAKTLAA-GKVIAKKLPKPLEKS
          KTSMA....V.VATAA.SKP.LR..VALGD.GNK.SEQPQA.M.LKK..K......K...KKLPKPLEKS
Retrocopy KTSMAGARWVAVATAAASKPRLRSKVALGDTGNKASEQPQAEMSLKKGNKNFSCWDKLLPKKLPKPLEKS

Parental  PLP--EPELEPEPVKEEKLSPEPILVDTPSLSPMETSGCA-PAEEYLCQAFSDVILAVSDVDAEDGADPN
          PLP...PEL...P..EEKLSPEP..V.TPSLSP.ETSG.A.P..E.LCQAFSDVILAVSDV.AEDGADPN
Retrocopy PLPKPDPELQSQPAEEEKLSPEPVSVATPSLSPLETSGRA<PVKEHLCQAFSDVILAVSDVNAEDGADPN

Parental  LCSEYVKDIYSYLRQLEEEQSVRPKYLVGREVTGNMRAILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQ
          L.SEYVKDI..YLRQL.EE..VR.KY..G.EVT.NM.A.LID.LVQVQMKFRLLQET.YMTVS..D..MQ
Retrocopy LFSEYVKDINAYLRQLVEE*VVRLKYPMGGEVTENMMAVLIDRLVQVQMKFRLLQETTYMTVSVVDQLMQ

Parental  NNCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDHTYTKHQIRQMEMKI
          N.CVPKKM...V.VT..FIASKYE...PPE...FAFVTDHT.TK.QI.QMEMKI
Retrocopy NHCVPKKMSHWVAVTTVFIASKYEGVHPPEVDNFAFVTDHT*TKYQISQMEMKI

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_176 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 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014239	2 retrocopies	retro_btau_1317, retro_btau_600,
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Erinaceus europaeus	ENSEEUG00000005724	2 retrocopies	retro_eeur_386, retro_eeur_548,
Felis catus	ENSFCAG00000001572	1 retrocopy	retro_fcat_840,
Myotis lucifugus	ENSMLUG00000012856	1 retrocopy	retro_mluc_1020,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Mus musculus	ENSMUSG00000041431	5 retrocopies	retro_mmus_1170, retro_mmus_1550, retro_mmus_2508, retro_mmus_2615, retro_mmus_3023,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176 ,
Rattus norvegicus	ENSRNOG00000018635	2 retrocopies	retro_rnor_568, retro_rnor_814,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,
Tarsius syrichta	ENSTSYG00000008928	1 retrocopy	retro_tsyr_232,
Tursiops truncatus	ENSTTRG00000002874	2 retrocopies	retro_ttru_524, retro_ttru_59,