RetrogeneDB ID: retro_vpac_346

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_109251:5..731(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUFM
• Ensembl ID: ENSVPAG00000009541
• Aliases: None
• Description: Tu translation elongation factor, mitochondrial [Source:HGNC Symbol;Acc:12420]

Sequence

>retro_vpac_346
CACGTTGAGTATGAAACTGAAACAAGACACTATGCCCACGTTGACTGTCCTGGTCACTCTGACTACATCAAGAACATGAT
TATTGGTGCTGCTCAAGTGGATGGTGCTATTCTTGTTGTTTCGGCAACTGACGGTCCTATGCCTCAAACAAGAGAACACA
TTCTTTTGGCTAAGCAAGTAGGTGTTCAAAGAATCATTGTCTTTTTAAACAAGTGTGATGTTGTTACAGATCCTGAAATG
CTTGACCTTGTTGAAATGGAGGTAAAGGAACTTCTTTCTTCATATGACTTTGACGGAGACAACACCCCCGTTATCAGAGG
ATCAGCACTTAAGGCTTTGGAAGGTGATCCTGCTTTTGAAGCTAAGATTCAAGAACTTCTAAATCAACTAGACACTTACG
TACCTGTACCTACTAGAGAAATTGACAAGCCTTTCTTGCTGTCTATCGAAGATGTCTTGACTATTACTGGTAGAGGGACT
GTTGTTACAGGTAGATGTGAAAGAGGTCAACTTAAGGTAGGCGAAGAAGTTGAAATTGTAGGTATTAAGGAAACTACAAA
AGCAGTTGTTACAGGAATTGAAATGTTTAGAAAACCTCTAGAAGAAGTTCTTCCGGGGGACAATGCTGGGATATTGTTGA
GAGGGATTGAAAAAGATGCTGTAACAAGAGGTCAAGTGTTAGCTAAACCTAAGTCAATTACTCCTCACTCTAAGTTCAAA
GCAGAG

Alignment

ORF - retro_vpac_346 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.38 %
• Parental protein coverage: 88.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HVEYSTAARHYAHTDCPGHADYVKNMITGTAPLDGCILVVAANDGPMPQTREHLLLAKQIGLEHV-VYVN
          HVEY.T..RHYAH.DCPGH.DY.KNMI.G.A..DG.ILVV.A.DGPMPQTREH.LLAKQ.G.....V..N
Retrocopy HVEYETETRHYAHVDCPGHSDYIKNMIIGAAQVDGAILVVSATDGPMPQTREHILLAKQVGVQRIIVFLN

Parental  KADAVQNSE-IELVELEIRELLTE-GYKGEETPVIVGSALCALEQRDPELGLKSVQKLLDAVDTYIPVPT
          K.D.V...E...LVE.E..ELL......G..TPVI.GSAL.ALE..DP....K..Q.LL...DTY.PVPT
Retrocopy KCDVVTDPEMLDLVEMEVKELLSSYDFDGDNTPVIRGSALKALEG-DPAFEAK-IQELLNQLDTYVPVPT

Parental  RDLEKPFLLPIESVYSIPGRGTVVTGTLERGILKKGDECEFLGHSKNIRTVVTGIEMFHKSLERAEAGDN
          R...KPFLL.IE.V..I.GRGTVVTG..ERG.LK.G.E.E..G.......VVTGIEMF.K.LE....GDN
Retrocopy REIDKPFLLSIEDVLTITGRGTVVTGRCERGQLKVGEEVEIVGIKETTKAVVTGIEMFRKPLEEVLPGDN

Parental  LGALVRGLKREDLRRGLVMAKPGSIQPHQNVEAQ
          .G.L.RG.......RG.V.AKP.SI.PH....A.
Retrocopy AGILLRGIEKDAVTRGQVLAKPKSITPHSKFKAE

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_346 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_346 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016474	1 retrocopy	retro_dord_278,
Homo sapiens	ENSG00000178952	1 retrocopy	retro_hsap_1816,
Macropus eugenii	ENSMEUG00000011131	1 retrocopy	retro_meug_1783,
Monodelphis domestica	ENSMODG00000015564	1 retrocopy	retro_mdom_384,
Mus musculus	ENSMUSG00000073838	1 retrocopy	retro_mmus_10,
Ornithorhynchus anatinus	ENSOANG00000013114	1 retrocopy	retro_oana_36,
Oryctolagus cuniculus	ENSOCUG00000002683	1 retrocopy	retro_ocun_333,
Pan troglodytes	ENSPTRG00000007939	1 retrocopy	retro_ptro_1174,
Rattus norvegicus	ENSRNOG00000018604	1 retrocopy	retro_rnor_1134,
Vicugna pacos	ENSVPAG00000009541	1 retrocopy	retro_vpac_346 ,
Drosophila melanogaster	FBgn0033184	1 retrocopy	retro_dmel_52,