RetrogeneDB ID: retro_vpac_562

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_46423:3296..4073(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5B
• Ensembl ID: ENSVPAG00000004025
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide [Source:HGNC Symbol;Acc:830]

Sequence

>retro_vpac_562
GGTCAGATGAATGAGGTCCCTGGAGCTAGGTTGAGGGTAGCCTTCTCAGGTTTGACTATGGCTGAATACTTTAGGGATGA
TCTTTCAAAAGACGTGTTGCTCTTTATCGACAATATCTTTCGGTTTTCGCAGGCAGGTTCTGAGATCTCAGCTTTGTTAG
GTAGAACTCCTTCGGCTGTGGGGTATCAGCCCACATTGGCTTACGAGATGGGCAAACTCCAAGAACGTATCACTTCTACA
AAGACAGGATCTATTACCTCAGTTCAGGCTGTCTATGTCCCTGCAGATGACCTTACTGACCCTGCTCCTGCTGCTATATT
TGCCCACCTGGATGCAAAGATTGTCCTAGACAGAAAGATCGCAGCCTTAGGACTCTATCCTGCTATTTCTCCGCTGCTGT
CCTCTTCTAACTTATTAACACCTAGAATTGTCGGGGAGGAACATTACTTCGTTGCCGAAGAGGTAGTTAGGGTATTGCAG
AAGTATGACGAGCTGCAAGACATCATCTCTATTTTGGGCATTGATGAATTAAGCGATGAAGACAAAAAACTTGTTTATAG
AGCTAGAAAGATTAGAAACTTTTTTTCTCAACCTTTCTTTGTAGCTGAGAAGTTCACCAATATTAACGGTAAGTACCTAA
CTAGAGAAGATACCCTTAGGTCTTTTAAGGCCATACTAGATGGTGAAGCTGATGATCTTCCTGAGGAAGCTTTCTTTTAT
GTAGGTAATATAGATGAAGCTAGAGAGAAAGCTAAGACCATGACAGAAGAAGATTCT

Alignment

ORF - retro_vpac_562 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.8 %
• Parental protein coverage: 53.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDM
          GQMNE.PGAR.RVA..GLT.AEYFRD....DVLLFIDNIFRF.QAGSE.SALLGR.PSAVGYQPTLA..M
Retrocopy GQMNEVPGARLRVAFSGLTMAEYFRDDLSKDVLLFIDNIFRFSQAGSEISALLGRTPSAVGYQPTLAYEM

Parental  GTMQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMD
          G..QERIT.TK.GSITSVQA.YVPADDLTDPAPA..FAHLDA..VL.R.IA.LG.YPA..PL.S.S....
Retrocopy GKLQERITSTKTGSITSVQAVYVPADDLTDPAPAAIFAHLDAKIVLDRKIAALGLYPAISPLLSSSNLLT

Parental  PNIVGNEHYEVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEVFTGHLG
          P.IVG.EHY.VA..V...LQ.Y..LQDII.ILG.DELS.EDK..V.RARKI..F.SQPF.VAE.FT...G
Retrocopy PRIVGEEHYFVAEEVVRVLQKYDELQDIISILGIDELSDEDKKLVYRARKIRNFFSQPFFVAEKFTNING

Parental  KLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHS
          K......T...F..IL.GE.D.LPE.AF..VG.I.EA..KA....EE.S
Retrocopy KYLTREDTLRSFKAILDGEADDLPEEAFFYVGNIDEAREKAKTMTEEDS

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_562 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_562 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 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016752	1 retrocopy	retro_acar_181,
Bos taurus	ENSBTAG00000013315	1 retrocopy	retro_btau_1264,
Choloepus hoffmanni	ENSCHOG00000005350	1 retrocopy	retro_chof_1544,
Callithrix jacchus	ENSCJAG00000033571	2 retrocopies	retro_cjac_1488, retro_cjac_928,
Dasypus novemcinctus	ENSDNOG00000011289	1 retrocopy	retro_dnov_361,
Echinops telfairi	ENSETEG00000010208	1 retrocopy	retro_etel_2162,
Homo sapiens	ENSG00000110955	1 retrocopy	retro_hsap_2128,
Gorilla gorilla	ENSGGOG00000011596	1 retrocopy	retro_ggor_1648,
Macropus eugenii	ENSMEUG00000002875	6 retrocopies	retro_meug_1416, retro_meug_1608, retro_meug_411, retro_meug_430, retro_meug_685, retro_meug_908,
Microcebus murinus	ENSMICG00000001084	1 retrocopy	retro_mmur_495,
Macaca mulatta	ENSMMUG00000001027	1 retrocopy	retro_mmul_103,
Pongo abelii	ENSPPYG00000004668	2 retrocopies	retro_pabe_1921, retro_pabe_2032,
Pan troglodytes	ENSPTRG00000005107	1 retrocopy	retro_ptro_1557,
Sus scrofa	ENSSSCG00000000405	1 retrocopy	retro_sscr_453,
Tarsius syrichta	ENSTSYG00000009962	1 retrocopy	retro_tsyr_644,
Tursiops truncatus	ENSTTRG00000002144	1 retrocopy	retro_ttru_371,
Vicugna pacos	ENSVPAG00000004025	2 retrocopies	retro_vpac_405, retro_vpac_562 ,