RetrogeneDB ID: retro_vpac_282

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3642:1795712..1796108(-)
• Located in intron of: ENSVPAG00000003779

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5G1
• Ensembl ID: ENSVPAG00000007653
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9) [Source:HGNC Symbol;Acc:841]

Sequence

>retro_vpac_282
GTGCAGACTACTAGAACACTACTCATTCCCCTGGCACTGATCTACCATTGAACATGGGGTCTAATCAGGCTTGTGTCTGC
CTCCTTTCAAGTAGGCCAGAGATCCCATCTACACAGCCTTTCTGTAGCAGCTCCTCATTCTAGGTAGCTCATTGAGAGTC
CCATACCAGTGTTGTCTCCCTGGACACTGACTCAGCAGCCAAGCTTATTGCTGCTGGGAAAACCATAGTTGATATGGCCG
GTTCAGAGGCCAGCCCTGGAACAGTGTTCCACAGCTTGATGCTTGGGTGTGCCAGGAACCTGCCTCTCAAACAGCAGGTC
TTTTTCCTATGCCATTCTGGGCTTTGCCCTGTCTGATGCCACAGGGCTTTTCTATCTTATGGTTGTCTTCCTCCTC

Alignment

ORF - retro_vpac_282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.93 %
• Parental protein coverage: 97.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQTTRALLIPPALIRSCTRGLIRPVSASFL-SRPEIPSEQPSNSSILLQVARREFQTSVVSRDIDTAAKF
          .QTTR.LLIP.ALI...T.GLIR.VSASF..SRPEIPS.QP..SS....VA..E..TSVVS.D.D.AAK.
Retrocopy VQTTRTLLIPLALIYH*TWGLIRLVSASFQ<SRPEIPSTQPFCSSSSF*VAH*ESHTSVVSLDTDSAAKL

Parental  IGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQL-FSYAILGFALSEAMGLFCLMVAFLI
          I.AG...V..AGS.A..GTVF.SL..G.ARN..LKQQ..FSYAILGFALS.A.GLF.LMV.FL.
Retrocopy IAAGKTIVDMAGSEASPGTVFHSLMLGCARNLPLKQQV>FSYAILGFALSDATGLFYLMVVFLL

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_282 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_282 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 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006341	1 retrocopy	retro_acar_9,
Bos taurus	ENSBTAG00000018339	3 retrocopies	retro_btau_1506, retro_btau_423, retro_btau_431,
Callithrix jacchus	ENSCJAG00000007352	7 retrocopies	retro_cjac_1190, retro_cjac_1549, retro_cjac_161, retro_cjac_1878, retro_cjac_289, retro_cjac_4060, retro_cjac_679,
Cavia porcellus	ENSCPOG00000009017	2 retrocopies	retro_cpor_43, retro_cpor_550,
Macropus eugenii	ENSMEUG00000005744	2 retrocopies	retro_meug_1650, retro_meug_1973,
Macaca mulatta	ENSMMUG00000013395	1 retrocopy	retro_mmul_173,
Oryctolagus cuniculus	ENSOCUG00000016225	2 retrocopies	retro_ocun_346, retro_ocun_375,
Otolemur garnettii	ENSOGAG00000011713	3 retrocopies	retro_ogar_1847, retro_ogar_2767, retro_ogar_531,
Rattus norvegicus	ENSRNOG00000007235	5 retrocopies	retro_rnor_1342, retro_rnor_2240, retro_rnor_529, retro_rnor_64, retro_rnor_880,
Sus scrofa	ENSSSCG00000017544	1 retrocopy	retro_sscr_348,
Tursiops truncatus	ENSTTRG00000008526	1 retrocopy	retro_ttru_279,
Vicugna pacos	ENSVPAG00000000409	1 retrocopy	retro_vpac_105,
Vicugna pacos	ENSVPAG00000007653	1 retrocopy	retro_vpac_282 ,