RetrogeneDB ID: retro_pcap_451

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_94416:8899..9624(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000010687
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDHA1
• Ensembl ID: ENSPCAG00000004196
• Aliases: None
• Description: pyruvate dehydrogenase (lipoamide) alpha 1 [Source:HGNC Symbol;Acc:8806]

Sequence

>retro_pcap_451
GTAGCATCTCGTACTGCCCAGAAGCCTGCTGGCAGAGTGCTGATGGCATCTTGTAATTCTGTAAACAACGTACATTTGAA
ATAAGAAATGTAATCTCCAGGGGTTAGAAGAGGACCTCTCCTCACAAGTGTCCTCAAGAAGGATGGACTCAGTGCTACAA
GGCGATGCACACTGTTTCCCTAATAGGGTAGAGACAGATCAGCTGTATAAACAAAAAAATTACTCGTGGTTTCTGTCACA
TGTGTGATGGTCAGGAAGTTTGTTGTGTGGGGCTTGAGGCTAGTGTGACTCCCACAGATCAAAACACTACAGCTAGTGGG
CTCATGGCTTTAGTTTTACTTGTGGTTTCACTGTTGCGCCGATTCTGACATAGCTTGCAAGACATAAAGAAGAGACTGCA
CTAAAAGGCAGGTGCCTATGCATGCTGTCTACGCATGCTGAGAACTTCCACAGAAGCAAAGACTCTGCTGGAGCTCAGGT
GTCCCTGGAAGCTGCCACTGCTCTGGCTAGTAAGCATAACAGAAAAAGATGAGGTACTTGTGACTCTGTATGGCAATGGC
ACTGCTAATCAGGTCAGACAGCTGAAGCTTGTTAACACGGCACCACGGTAAAAACTACCTTTTATTTTCCTCTGTGAGAA
TAACTGCTACGGAATGGGAACATCTGTTGAGACAGCAGCAGCCAGCACTGACAAGGAAAGAGGGAATCTGACTCCTGGAC
TAAGA

Alignment

ORF - retro_pcap_451 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.94 %
• Parental protein coverage: 62.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  VLSGAAQKPASRVLVASRNFANDA-TFEI-KKCDLHRLEE-GPPVTTVLTREDGL-RYYRMMQTVRRM-E
          V.S..AQKPA.RVL.AS.N..N...TFEI.KKC.L..LEE.GP..T.VL...DGL...Y..M.TV.....
Retrocopy VASRTAQKPAGRVLMASCNSVNNV<TFEI<KKCNLQGLEE<GPLLTSVL-KKDGL<QCYKAMHTVSLI<R

Parental  LKADQLYKQK-IIRGFCHLCDGQEACCVGLEAGINPTDHLITAYR-AHGFTFTRGLSVREILAELTGRRG
          ...DQLYKQK.I.RGFCH.CDGQE.CCVGLEA...PTD...TA...AHGF.FT.G..V..IL..L.....
Retrocopy VETDQLYKQK>ITRGFCHMCDGQEVCCVGLEASVTPTDQNTTASG<AHGFSFTCGFTVAPILT*LARHKE

Parental  GCA-KGKGGSM-HMYAKNFYGGNGIVGAQVPLGAGIALACKYNGK-DEVCLTLYGDGAANQGQIFEAYNM
          ..A.KG....M....A.NF.......GAQV.L.A..ALA.K.N.K.DEV..TLYG.G.ANQ.......N.
Retrocopy ETALKGRCLCMLSTHAENFHRSKDSAGAQVSLEAATALASKHNRK>DEVLVTLYGNGTANQVRQLKLVNT

Parental  AALWKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLR
          A...KLP.IF.CENN.YGMGTSVE.AAASTD...RG...PGLR
Retrocopy APR*KLPFIFLCENNCYGMGTSVETAAASTD-KERGNLTPGLR

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_451 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000001392	1 retrocopy	retro_etel_1802,
Loxodonta africana	ENSLAFG00000009426	1 retrocopy	retro_lafr_91,
Macaca mulatta	ENSMMUG00000017336	1 retrocopy	retro_mmul_123,
Procavia capensis	ENSPCAG00000004196	1 retrocopy	retro_pcap_451 ,
Sarcophilus harrisii	ENSSHAG00000015375	1 retrocopy	retro_shar_84,