RetrogeneDB ID: retro_pcap_112

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_6823:39884..40368(+)
• Located in intron of: ENSPCAG00000001257

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFAND5
• Ensembl ID: ENSPCAG00000007436
• Aliases: None
• Description: zinc finger, AN1-type domain 5 [Source:HGNC Symbol;Acc:13008]

Sequence

>retro_pcap_112
GGGACAGCTAAGGGTTCTCATGACTTATCTCAGATTCTGTATCTGTACAGACAGTGGACACTGGTTTAAACACTGTGAAG
GAGCTGCTGGCAGCACATCTGAAAATCAAGAAATGTGCTACGGCCGCCTTGCCTGTAACTCAGCAAATGACCGAAATGAG
CATTTCAAGAGAGGACAAACTAACTACTCTGAAAACAGAGGTATTGGAGCCAGCTGTCACTCAACCCAGTCCATCAGTTT
CTCAGTTAGTACTTCTCAAAGTGAAGAAAAAGCTCCTGAGTTGCCCAAACCAAAGAAGAACAGATGTTTCATGTGCAGGA
AGAAGGTTGGCCTCACAGGGTTTGACTGCCGATGTGGAAATTTGTTTTGCAGACTTCACCATTGCTCTGACAAGCACAAC
TGTCCATATGATTACAAAGCAGAGGCTGCAGCAAAAATTAGAAAAGAGAATCCAGTTGTTGTGGCTGAAAAAATCCAGAG
AATA

Alignment

ORF - retro_pcap_112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.12 %
• Parental protein coverage: 85.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GTASGSNSPT-SDSASVQRADTSLN-NCEGAAGSTSE-KSRNV-PVAALPVTQQMTEMSISREDKITTPK
          GTA.GS.....SDS.SVQ..DT.LN..CEGAAGSTSE.KSRNV...AALPVTQQMTEMSISREDK.TT.K
Retrocopy GTAKGSHDLS<SDSVSVQTVDTGLN<HCEGAAGSTSE<KSRNV<ATAALPVTQQMTEMSISREDKLTTLK

Parental  TEVSEPVVTQPSPSVSQ-PSTSQSEEKAPELPKPKKNRCFMCRKKVGLTGFDCRCGNLFCGLHRYSDKHN
          TEV.EP.VTQPSPSVSQ..STSQSEEKAPELPKPKKNRCFMCRKKVGLTGFDCRCGNLFC.LH..SDKHN
Retrocopy TEVLEPAVTQPSPSVSQ<VSTSQSEEKAPELPKPKKNRCFMCRKKVGLTGFDCRCGNLFCRLHHCSDKHN

Parental  CPYDYKAEAAAKIRKENPVVVAEKIQRI
          CPYDYKAEAAAKIRKENPVVVAEKIQRI
Retrocopy CPYDYKAEAAAKIRKENPVVVAEKIQRI

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_112 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002366	2 retrocopies	retro_chof_1050, retro_chof_1846,
Cavia porcellus	ENSCPOG00000005076	2 retrocopies	retro_cpor_1398, retro_cpor_774,
Felis catus	ENSFCAG00000027317	1 retrocopy	retro_fcat_641,
Homo sapiens	ENSG00000107372	1 retrocopy	retro_hsap_2063,
Gorilla gorilla	ENSGGOG00000008957	1 retrocopy	retro_ggor_1485,
Myotis lucifugus	ENSMLUG00000007173	2 retrocopies	retro_mluc_1233, retro_mluc_1993,
Monodelphis domestica	ENSMODG00000004426	1 retrocopy	retro_mdom_1910,
Mustela putorius furo	ENSMPUG00000008951	1 retrocopy	retro_mputfur_143,
Mus musculus	ENSMUSG00000024750	1 retrocopy	retro_mmus_1176,
Oryctolagus cuniculus	ENSOCUG00000000795	1 retrocopy	retro_ocun_1546,
Procavia capensis	ENSPCAG00000007436	1 retrocopy	retro_pcap_112 ,
Pongo abelii	ENSPPYG00000019290	1 retrocopy	retro_pabe_1676,
Vicugna pacos	ENSVPAG00000000700	1 retrocopy	retro_vpac_23,