RetrogeneDB ID: retro_vpac_446

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_2006:187249..187744(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC53
• Ensembl ID: ENSVPAG00000002010
• Aliases: None
• Description: coiled-coil domain containing 53 [Source:HGNC Symbol;Acc:24256]

Sequence

>retro_vpac_446
AATCTGTGGTACATACACACTGTACAGTTCTTCAACCACTTTTCTACTGGTTGTGAAGAGAAACTGGCAGACCTTTCTCT
TTGTCTGCAGCAAACTGAAACAACTCTCAGTATTTTAGATGCAAAGTTGTCATCTATTCCAGGCCTAGATGATGTCACAT
TTGAAGTCAGCCCCTATAAGTGATACCTAGACGGTATCACAAATCAATCTCAGTCTGTGATCACTTTGGAGTGATCACAG
CAGAAGAGTTTACACGACTCTGGACCACAGGAAAGTAAAGTAACACCAGAAAATATCTTAACTGTCGCCAAGGATCCAAG
ATACGCCAGGTATCTCAAAACAGTTGAAGTCGGTGTTCCGGTGATGGCAATAAGAAATAAAATGATATCAGAAGGACTAG
ACCCAGACCTTGAGAGGTCAGATGCTCCAGAGCCTGATGGTGAAGGTGAAGAAAATACAGAAGAAAGTCCTGGTAGCGAA
TCTTCTTTTAGTGAC

Alignment

ORF - retro_vpac_446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.31 %
• Parental protein coverage: 84.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NQFVVHTVQFLNRFSTVCEEKLADLSLRIQQIETTLNILDAKLSSIPGLDDVTFEVSPIS--VSSITNES
          N....HTVQF.N.FST.CEEKLADLSL..QQ.ETTL.ILDAKLSSIPGLDDVTFEVSP.......ITN.S
Retrocopy NLWYIHTVQFFNHFSTGCEEKLADLSLCLQQTETTLSILDAKLSSIPGLDDVTFEVSPYK*YLDGITNQS

Parental  HSVTTSEQPQQNSLQDSGPQESEVTPENILTVAKDPRYARYLKMVQVGCPVMAIRNKMISEGLDPDLLER
          .SV.T.E..QQ.SL.DSGPQES.VTPENILTVAKDPRYARYLK.V.VG.PVMAIRNKMISEGLDPD.LER
Retrocopy QSVITLE*SQQKSLHDSGPQESKVTPENILTVAKDPRYARYLKTVEVGVPVMAIRNKMISEGLDPD-LER

Parental  PDAPVPDGEGEKNTEESSDSESSFSD
          .DAP.PDGEGE.NTEES..SESSFSD
Retrocopy SDAPEPDGEGEENTEESPGSESSFSD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_446 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_446 was not experimentally validated.

Homology

Retrocopy orthology:

Vicugna pacos 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 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006329	1 retrocopy	retro_amel_791,
Canis familiaris	ENSCAFG00000007270	2 retrocopies	retro_cfam_53, retro_cfam_550,
Callithrix jacchus	ENSCJAG00000014225	1 retrocopy	retro_cjac_4073,
Echinops telfairi	ENSETEG00000002254	1 retrocopy	retro_etel_1917,
Felis catus	ENSFCAG00000019358	1 retrocopy	retro_fcat_498,
Homo sapiens	ENSG00000120860	1 retrocopy	retro_hsap_4696,
Gorilla gorilla	ENSGGOG00000014975	1 retrocopy	retro_ggor_2922,
Loxodonta africana	ENSLAFG00000007850	1 retrocopy	retro_lafr_761,
Macropus eugenii	ENSMEUG00000004888	3 retrocopies	retro_meug_1441, retro_meug_576, retro_meug_629,
Monodelphis domestica	ENSMODG00000002579	1 retrocopy	retro_mdom_959,
Mus musculus	ENSMUSG00000020056	1 retrocopy	retro_mmus_1773,
Nomascus leucogenys	ENSNLEG00000006365	1 retrocopy	retro_nleu_2366,
Otolemur garnettii	ENSOGAG00000003322	2 retrocopies	retro_ogar_3267, retro_ogar_738,
Pongo abelii	ENSPPYG00000004878	1 retrocopy	retro_pabe_3649,
Pan troglodytes	ENSPTRG00000005358	1 retrocopy	retro_ptro_3121,
Ictidomys tridecemlineatus	ENSSTOG00000001870	1 retrocopy	retro_itri_970,
Tupaia belangeri	ENSTBEG00000008498	3 retrocopies	retro_tbel_1036, retro_tbel_1165, retro_tbel_2967,
Tarsius syrichta	ENSTSYG00000000587	4 retrocopies	retro_tsyr_1100, retro_tsyr_265, retro_tsyr_443, retro_tsyr_955,
Tursiops truncatus	ENSTTRG00000017221	4 retrocopies	retro_ttru_1569, retro_ttru_1865, retro_ttru_1919, retro_ttru_935,
Vicugna pacos	ENSVPAG00000002010	1 retrocopy	retro_vpac_446 ,