RetrogeneDB ID: retro_vpac_521

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_2993:113520..113878(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB1
• Ensembl ID: ENSVPAG00000006517
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 1 [Source:HGNC Symbol;Acc:9537]

Sequence

>retro_vpac_521
CGGAGCCGCTCCTCAGAGTCTCACAGCCCGGCCGCCCCGTGCGGCTGCGCAGTTCGCCCCTCGCGCTCGGCGGAGCTCTG
TATTGGCAATGGCTGGGGGAAACTTTTCAGTTACTGCTTCTGATACGTGACTGAGTGAAGGCTTTTCAACCTGACGCGGC
CCCAAATGTTACGAATTAACAAAACAGTCCTTGAATGCAGCATTTTTCATAGAGAATGTTTCACTGACAAAGACTACTGA
AGCAAGACTAAAGATGTATAAGCAATCTAATATGAAGGCCATGACTGGGGCCAAAGCTGCAATGCTGTTTACAATCCTCA
ACTTAAGATGCTTCTTTTTATACTGTGTTTACATCATC

Alignment

ORF - retro_vpac_521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.54 %
• Parental protein coverage: 51.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RDMAMEPHGVAGP-LQLRFSPYAFNGG-TVLAIAGEDFSIVASDTRLSEGFSIHTRDSPKCYKLTDRTVI
          R....E.H..A.P...LR.SP.A..G...VLA.AG..FS..ASDT.LSEGFS..T...PKCY.LT.....
Retrocopy RSRSSESHSPAAP<VRLRSSPLALGGA<SVLAMAGGNFSVTASDT*LSEGFS--T*RGPKCYELTKQSLN

Parental  GCSGFHGDCLTLTKIIEARLKMYQHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNI
          ....F......LTK..EARLKMY..SN.KAM.TGA.AAML.TIL..R.FF.Y.VY.I
Retrocopy --AAFFIENVSLTKTTEARLKMYKQSNMKAM-TGAKAAMLFTILNLRCFFLYCVYII

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_521 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_521 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 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017047	1 retrocopy	retro_amel_1066,
Canis familiaris	ENSCAFG00000004116	1 retrocopy	retro_cfam_2108,
Callithrix jacchus	ENSCJAG00000020644	1 retrocopy	retro_cjac_632,
Dasypus novemcinctus	ENSDNOG00000019502	1 retrocopy	retro_dnov_2087,
Felis catus	ENSFCAG00000031269	1 retrocopy	retro_fcat_911,
Gorilla gorilla	ENSGGOG00000022128	1 retrocopy	retro_ggor_1661,
Microcebus murinus	ENSMICG00000007469	1 retrocopy	retro_mmur_173,
Macaca mulatta	ENSMMUG00000019919	1 retrocopy	retro_mmul_1135,
Mustela putorius furo	ENSMPUG00000007150	1 retrocopy	retro_mputfur_1196,
Mus musculus	ENSMUSG00000014769	2 retrocopies	retro_mmus_1784, retro_mmus_3664,
Oryctolagus cuniculus	ENSOCUG00000007973	2 retrocopies	retro_ocun_1029, retro_ocun_620,
Procavia capensis	ENSPCAG00000000344	1 retrocopy	retro_pcap_329,
Pongo abelii	ENSPPYG00000017191	1 retrocopy	retro_pabe_130,
Vicugna pacos	ENSVPAG00000006517	1 retrocopy	retro_vpac_521 ,