RetrogeneDB ID: retro_pcap_394

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_67271:1414..1712(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBCA
• Ensembl ID: ENSPCAG00000011849
• Aliases: None
• Description: tubulin folding cofactor A [Source:HGNC Symbol;Acc:11579]

Sequence

>retro_pcap_394
CAGCTCACAATTAAAACCAGCATTAGGAAATGATTAGTCAAAGTGATGCATGAAGAAGAAGCAAAACAACAAGGAGTAAA
AATTGAGACAATGAGAGCTGAAGATGCTGAATATTTTGTCGTTAAAAAGCAGACAGAAATCTTGCAAGCATCCTGGATGA
TGAAGCCAGATTGCAAGCACAGGTTGGAAAGCCCATATGCTGATCTTCTGCAGGTACTAGAAAGTGAAAAAAGAGTTGGA
GGAAGCTAAAGAATACAAAGAAGCTCTTTCAGTACTGGTTTCAGTGAAGGTAGAAGCC

Alignment

ORF - retro_pcap_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.63 %
• Parental protein coverage: 75.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QIKIKTGVVKRLVKEKVMYEKEAKQQEEKIEKMRAEDGENYAIKKQAEILQESRMMIPDCQRRLETAYAD
          Q..IKT...K.LVK..VM.E.EAKQQ..KIE.MRAED.E....KKQ.EILQ.S.MM.PDC..RLE..YAD
Retrocopy QLTIKTSIRK*LVK--VMHEEEAKQQGVKIETMRAEDAEYFVVKKQTEILQASWMMKPDCKHRLESPYAD

Parental  LLQLLESE-KELEEAEEYKEARSVLDSVKLEA
          LLQ.LESE.KELEEA.EYKEA.SVL.SVK.EA
Retrocopy LLQVLESE>KELEEAKEYKEALSVLVSVKVEA

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_394 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014223	4 retrocopies	retro_acar_11, retro_acar_130, retro_acar_142, retro_acar_195,
Choloepus hoffmanni	ENSCHOG00000002112	2 retrocopies	retro_chof_1592, retro_chof_304,
Callithrix jacchus	ENSCJAG00000019848	4 retrocopies	retro_cjac_114, retro_cjac_2160, retro_cjac_2173, retro_cjac_2974,
Loxodonta africana	ENSLAFG00000005316	1 retrocopy	retro_lafr_1212,
Macaca mulatta	ENSMMUG00000011853	1 retrocopy	retro_mmul_229,
Procavia capensis	ENSPCAG00000011849	1 retrocopy	retro_pcap_394 ,
Rattus norvegicus	ENSRNOG00000048342	1 retrocopy	retro_rnor_140,
Vicugna pacos	ENSVPAG00000001561	1 retrocopy	retro_vpac_277,