RetrogeneDB ID: retro_vpac_464

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_22166:1030..1345(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STYX
• Ensembl ID: ENSVPAG00000012229
• Aliases: None
• Description: serine/threonine/tyrosine interacting protein [Source:HGNC Symbol;Acc:11447]

Sequence

>retro_vpac_464
TTTATTGATGAGAGCTTACAAAGTGGAGGAAAAGTTCTTGTCCATGGGAATGGAGGGATCTCCAGGAGTGCTGCCTTTAT
TATTGCATACATTATGGTAACGTTTGGAATGAAGTACAGAGATGCATATGCCTACGTTCAAGAAAGAAGATTTTGTATTA
ATCCTAGTGCTGGATTTGTCCATCAACTTCAGGAATATGAAGCCATCTATTTAGAAAAATTAACAGTACAGATGATGTCG
CCACTTCAGATAGAAAGGTCGTTATCTGTTCATTCTGGTACCACAGGCAGTTTGAAGAGAACACATGAAGAAGAT

Alignment

ORF - retro_vpac_464 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 56.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FIDGSLQSGGKVLVHGNAGISRSAAFVIAYIMETFGMKYRDAFAYVQERRFCINPNAGFVHQLQEYEAIY
          FID.SLQSGGKVLVHGN.GISRSAAF.IAYIM.TFGMKYRDA.AYVQERRFCINP.AGFVHQLQEYEAIY
Retrocopy FIDESLQSGGKVLVHGNGGISRSAAFIIAYIMVTFGMKYRDAYAYVQERRFCINPSAGFVHQLQEYEAIY

Parental  LAKLTIQMMSPLQIERSLSVHSGTTGQLKRTHEEE
          L.KLT.QMMSPLQIERSLSVHSGTTG.LKRTHEE.
Retrocopy LEKLTVQMMSPLQIERSLSVHSGTTGSLKRTHEED

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_464 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_464 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 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016631	9 retrocopies	retro_dnov_1713, retro_dnov_1720, retro_dnov_1914, retro_dnov_2138, retro_dnov_2186, retro_dnov_2218, retro_dnov_2221, retro_dnov_461, retro_dnov_66,
Echinops telfairi	ENSETEG00000000561	1 retrocopy	retro_etel_1881,
Monodelphis domestica	ENSMODG00000029372	1 retrocopy	retro_mdom_44,
Mus musculus	ENSMUSG00000053205	1 retrocopy	retro_mmus_96,
Oryctolagus cuniculus	ENSOCUG00000029442	1 retrocopy	retro_ocun_1555,
Ochotona princeps	ENSOPRG00000016123	1 retrocopy	retro_opri_976,
Rattus norvegicus	ENSRNOG00000007956	1 retrocopy	retro_rnor_256,
Ictidomys tridecemlineatus	ENSSTOG00000014504	1 retrocopy	retro_itri_1365,
Vicugna pacos	ENSVPAG00000012229	1 retrocopy	retro_vpac_464 ,