RetrogeneDB ID: retro_vpac_342

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_1054:139874..140457(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3M
• Ensembl ID: ENSVPAG00000007791
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit M [Source:HGNC Symbol;Acc:24460]

Sequence

>retro_vpac_342
CAAAGTGATACTGCATCGAAAGTCATGGTAGAATTGCTAGGAAGTTAAACAGAGGACGGTGCTGCCCAGGCTCGAGTTGT
TGCCCACAGGTATACTGTGCAAGCATTGAAAAATCCAAATGCATTTCTCTTTGACCATCTTCTTACTTTAAAATCAATCA
AGTTTTTGGAAGGTGAGCTTATTTGTGATCTTTTAACCATTTTTGTGAGTGCTAAACAGCATCATATGTCAAATTTTAAC
AGAATAATGACTTCATTGAGTCACTTAATCTACTACAAGAACAGAATATGGCAGTAATGAGACTACCTATGGGAATGGCA
GTGGAAAATAAAGAAATTTCTTTTGACACAATGAAACAAGAACTTCAGATTAGAGCTATGATGTTGAAGCATTTCTTACT
GATGCAGTAAGAACTACAATGGTCTACTGCAAAATTGATCAAACCCAGAGAAAAGTGGTCGTCAGTTATAGCACACGCCA
TACATTTGGAAAACAACAATGAAAACAACTGTATGGCACACTCAATGGCTGGAAACAGAACTTGAACAAAGCGAAAAACA
GCCTTTTGAGTCTTTCTGATACC

Alignment

ORF - retro_vpac_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.5 %
• Parental protein coverage: 52.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KSDAASKVMVELLGSYTEDNASQARVDAHRCIVRALKDPNAFLFDHLLTLKPVKFLEGELIHDLLTIFVS
          .SD.ASKVMVELLGS.TED.A.QARV.AHR..V.ALK.PNAFLFDHLLTLK..KFLEGELI.DLLTIFVS
Retrocopy QSDTASKVMVELLGS*TEDGAAQARVVAHRYTVQALKNPNAFLFDHLLTLKSIKFLEGELICDLLTIFVS

Parental  AK-LASYVKFYQNNKDFIDSLGLLHEQNMAKMRLLTFMGMAVENKEISFDTMQQELQIGAD-DVEAFVID
          AK..ASYVKF.QNN.DFI.SL.LL.EQNMA.MRL...MGMAVENKEISFDTM.QELQI.A..DVEAF..D
Retrocopy AK<TASYVKF*QNN-DFIESLNLLQEQNMAVMRLP--MGMAVENKEISFDTMKQELQIRAM<DVEAFLTD

Parental  AVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQLYDTLNAWKQNLNKVKNSLLSLSDT
          AVRT.MVYCKIDQTQRKVVVS.ST..TFGKQQ..QLY.TLN.WKQNLNK.KNSLLSLSDT
Retrocopy AVRTTMVYCKIDQTQRKVVVSYSTRHTFGKQQ*KQLYGTLNGWKQNLNKAKNSLLSLSDT

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_342 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_342 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005338	2 retrocopies	retro_btau_1736, retro_btau_812,
Echinops telfairi	ENSETEG00000013437	1 retrocopy	retro_etel_120,
Myotis lucifugus	ENSMLUG00000014727	2 retrocopies	retro_mluc_1982, retro_mluc_431,
Mus musculus	ENSMUSG00000027170	1 retrocopy	retro_mmus_421,
Oryctolagus cuniculus	ENSOCUG00000004483	1 retrocopy	retro_ocun_282,
Otolemur garnettii	ENSOGAG00000015913	1 retrocopy	retro_ogar_1783,
Pteropus vampyrus	ENSPVAG00000015083	1 retrocopy	retro_pvam_1134,
Vicugna pacos	ENSVPAG00000007791	1 retrocopy	retro_vpac_342 ,