RetrogeneDB ID: retro_pcap_459

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_97502:5569..5934(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAA50
• Ensembl ID: ENSPCAG00000009780
• Aliases: None
• Description: N(alpha)-acetyltransferase 50, NatE catalytic subunit [Source:HGNC Symbol;Acc:29533]

Sequence

>retro_pcap_459
CTTGCATATTTCAGTGATACTGCAGTAGGTGTAATCTGATGTAGGGTGGATCATTTACAGAGTCAGAGAGACTTTACATT
GTGATGCTAGGATGCCTAGTACCTTAGTGAAGGCTAGAAACAGGTACTAAAATATTAAATCATGTCCTCAACATCTGTGA
AAAAGATGGCACTTTTGACAATATCTATCTGCATGTCCAAATCAGCAAAGAGTCAGCAATTGACTTCTACAGGAAGTTTG
GCTTTGAGTTTATCAAGACAAAGAAGAACTACTATAAGAGGATAGAGCCCGCAGATGCTCATGTGCTGCAGAAAAACCTT
AGAGTCCGTTCTGGACAGAATGCAGATGTGCAAAAGACAGACAAC

Alignment

ORF - retro_pcap_459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.85 %
• Parental protein coverage: 72.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAYFNDIAVGAVCCRVDHSQNQK-RLYIMTLGCLAPYRRLGIGTKMLNHVLDICEKDGTFDNIYLHIQIG
          LAYF.D.AVG...CRVDH.Q.Q..RLYI..LGCL.P..RL..GTK.LNHVL.ICEKDGTFDNIYLH.QI.
Retrocopy LAYFSDTAVGVI*CRVDHLQSQR<RLYIVMLGCLVP**RLETGTKILNHVLNICEKDGTFDNIYLHVQIS

Parental  TESEIDFYRKFGCEMNET----YWKTETTDTHVLQINLKAPSGQNADMQ-TDN
          .ES.IDFYRKFG.E...T....Y...E..D.HVLQ.NL...SGQNAD.Q.TDN
Retrocopy KESAIDFYRKFGFEFIKTKKNYYKRIEPADAHVLQKNLRVRSGQNADVQKTDN

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_459 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 17 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020261	2 retrocopies	retro_cjac_1941, retro_cjac_2823,
Cavia porcellus	ENSCPOG00000014169	6 retrocopies	retro_cpor_1027, retro_cpor_1028, retro_cpor_1199, retro_cpor_1200, retro_cpor_217, retro_cpor_480,
Dasypus novemcinctus	ENSDNOG00000001027	1 retrocopy	retro_dnov_2574,
Erinaceus europaeus	ENSEEUG00000014852	1 retrocopy	retro_eeur_547,
Homo sapiens	ENSG00000121579	1 retrocopy	retro_hsap_874,
Gorilla gorilla	ENSGGOG00000006589	2 retrocopies	retro_ggor_432, retro_ggor_710,
Loxodonta africana	ENSLAFG00000004023	1 retrocopy	retro_lafr_1159,
Monodelphis domestica	ENSMODG00000018160	1 retrocopy	retro_mdom_1645,
Nomascus leucogenys	ENSNLEG00000004624	1 retrocopy	retro_nleu_2586,
Oryctolagus cuniculus	ENSOCUG00000006467	2 retrocopies	retro_ocun_466, retro_ocun_984,
Otolemur garnettii	ENSOGAG00000011197	1 retrocopy	retro_ogar_157,
Ochotona princeps	ENSOPRG00000014309	1 retrocopy	retro_opri_1044,
Procavia capensis	ENSPCAG00000009780	2 retrocopies	retro_pcap_205, retro_pcap_459 ,
Pan troglodytes	ENSPTRG00000015233	2 retrocopies	retro_ptro_3015, retro_ptro_3031,
Sorex araneus	ENSSARG00000004134	1 retrocopy	retro_sara_447,
Ictidomys tridecemlineatus	ENSSTOG00000009438	1 retrocopy	retro_itri_1703,
Tursiops truncatus	ENSTTRG00000009849	3 retrocopies	retro_ttru_1729, retro_ttru_1814, retro_ttru_948,