RetrogeneDB ID: retro_vpac_47

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1209:452087..452355(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF1AX
• Ensembl ID: ENSVPAG00000009927
• Aliases: None
• Description: eukaryotic translation initiation factor 1A, X-linked [Source:HGNC Symbol;Acc:3250]

Sequence

>retro_vpac_47
AAGAGGCTATGCCATATCAAAGGAAAACTGAGAAGAATGGTTTAAATAAATACCTCAGAAATTTTATTAGTTGGTCTGCC
AGACTATCAGGATAGCAAAGCTGATGTAATTTTAAAATACAATGCAGGTGAAGCTAAAAATCCGAAGGAGTACGGCAAGC
TTGCAAACCACACTATTAAAATCAATGAAACAGATAGATTTGGCGCTGGAGATGATGATGCAATCCATTTGATGATATGA
AGATGATGATAAAGACCATGATGATATC

Alignment

ORF - retro_vpac_47 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.48 %
• Parental protein coverage: 64.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KRLCHIRGKLRKKVWINTSDIILVGLRD-QDNKADVILKYNADEARSLKAYGELPEHA-KINETDTFGPG
          KRLCHI.GKLR..V.INTS.I.LVGL.D.QD.KADVILKYNA.EA...K.YG.L..H..KINETD.FG.G
Retrocopy KRLCHIKGKLRRMV*INTSEILLVGLPDYQDSKADVILKYNAGEAKNPKEYGKLANHTIKINETDRFGAG

Parental  DDDEIQ-FDDI-GDDDEDIDDI
          DDD.I..FDD...DDD.D.DDI
Retrocopy DDDAIH<FDDM<EDDDKDHDDI

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_47 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_47 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 16 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017633	3 retrocopies	retro_btau_1293, retro_btau_293, retro_btau_381,
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Erinaceus europaeus	ENSEEUG00000007518	3 retrocopies	retro_eeur_408, retro_eeur_567, retro_eeur_686,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pongo abelii	ENSPPYG00000020176	1 retrocopy	retro_pabe_1185,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sorex araneus	ENSSARG00000013528	1 retrocopy	retro_sara_324,
Sarcophilus harrisii	ENSSHAG00000010995	1 retrocopy	retro_shar_707,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,
Tursiops truncatus	ENSTTRG00000002012	1 retrocopy	retro_ttru_1009,
Vicugna pacos	ENSVPAG00000009927	4 retrocopies	retro_vpac_47 , retro_vpac_531, retro_vpac_550, retro_vpac_590,