RetrogeneDB ID: retro_pcap_13

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_7136:11386..12151(-)
• Located in intron of: ENSPCAG00000008583

Retrocopy information

• Ensembl ID: ENSPCAG00000008698
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PGAM2
• Ensembl ID: ENSPCAG00000002181
• Aliases: None
• Description: phosphoglycerate mutase 2 (muscle) [Source:HGNC Symbol;Acc:8889]

Sequence

>retro_pcap_13
ACGGCTGCCTATCAGCTGGTGCTTATCCCGCACGGCGAGAGCGCCCGGAACCTAAAGAACCGTTTCAGCGGCTGGTACGA
TGCCGACCTGAGCCCGGCGGGGCAGGAGGAAGCAAAGCGCGGCGGGCAGGCGCTGGGAGATGCTGGCTACAAGTTTGACA
TCTGCTTCACTTCAGTGCAAAAGAGAGCAATCCGGACCCTCTGGGCAGTGCTGGACGCCACTGACCAGATGTGGCTGCCA
GTTGTGAGGACATGGCGCCTCAGTGAGCGGCACTATGGGGGTCCGACTGGCCTCAATAAAGCAGAAACTGCTGCCAAGCA
TGGTGAGGCCCAGGTAAAGATCTGGAGGCGTTCTTACGATGTCCCACCACCCCCGATGGAGCCTGACCACCCGTTCTACA
GCAACATCAGTAAGGACCGCAGGTATGCAGACCTCACTGAAGACCAGCTACCCTCCTGTGAGAGTCTAAAGGACACCATT
GCCAGAGCCCTGCCTTTTTGGAGTGAAGAAATAGTTCCTCAGATCAAGGAGGGGAAACGGGTACTGATTGCAGCGCATGG
CAACAGCCTTCAGGGCATTGTCAAACATCTGGAGGGTCTCTCTGAAGAGGCTATCTTGGAGCTGAACCTGCGCACTGGTA
TTCCCATTGTCTATGAACTGGACAAGAACTTGAAGCCCATCAAGCCCATGCAGTTCCTGGGAGATGAAGAGACGGTGCGT
AAAGCCATGGAAGCGGTGGCTGCCCAGGGCAAGGCCAAGAAGTAA

Alignment

ORF - retro_pcap_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.98 %
• Parental protein coverage: 99.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STHRLVIVRHGESTWNQENRFCGWFDAELSEKGVEEAKRGAQAIKDAKMEFDICYTSVLKRAIRTLWTIL
          ....LV...HGES..N..NRF.GW.DA.LS..G.EEAKRG.QA..DA...FDIC.TSV.KRAIRTLW..L
Retrocopy AAYQLVLIPHGESARNLKNRFSGWYDADLSPAGQEEAKRGGQALGDAGYKFDICFTSVQKRAIRTLWAVL

Parental  DGTDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEEQVKIWRRSFDIPPPPMDEKHPYYTTISKERR
          D.TDQMWLPVVRTWRL.ERHYGG.TGLNKAETAAKHGE.QVKIWRRS.D.PPPPM...HP.Y..ISK.RR
Retrocopy DATDQMWLPVVRTWRLSERHYGGPTGLNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKDRR

Parental  YAGLKTGELPTCESLKDTIARALPFWNEEIVPQIKAGKRVLIAAHGNSLRGIVKHLEGMSDQAIMELNLP
          YA.L....LP.CESLKDTIARALPFW.EEIVPQIK.GKRVLIAAHGNSL.GIVKHLEG.S..AI.ELNL.
Retrocopy YADLTEDQLPSCESLKDTIARALPFWSEEIVPQIKEGKRVLIAAHGNSLQGIVKHLEGLSEEAILELNLR

Parental  TGIPIVYELDNALKPTKPMRFLGDEETVRKAMEAVAAQGKAK
          TGIPIVYELD..LKP.KPM.FLGDEETVRKAMEAVAAQGKAK
Retrocopy TGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQGKAK

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_13 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 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024480	1 retrocopy	retro_dnov_34,
Macropus eugenii	ENSMEUG00000012920	8 retrocopies	retro_meug_1044, retro_meug_1303, retro_meug_1636, retro_meug_1838, retro_meug_202, retro_meug_2152, retro_meug_251, retro_meug_945,
Otolemur garnettii	ENSOGAG00000006713	1 retrocopy	retro_ogar_164,
Procavia capensis	ENSPCAG00000002181	1 retrocopy	retro_pcap_13 ,
Rattus norvegicus	ENSRNOG00000013532	1 retrocopy	retro_rnor_2889,
Tupaia belangeri	ENSTBEG00000004587	1 retrocopy	retro_tbel_3939,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,