RetrogeneDB ID: retro_vpac_52

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1271:697265..697929(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OLA1
• Ensembl ID: ENSVPAG00000009660
• Aliases: None
• Description: Obg-like ATPase 1 [Source:HGNC Symbol;Acc:28833]

Sequence

>retro_vpac_52
ATGCCTCCCAAAAAGGGAAGTGATGGAATTAAACCACCTCCAATCATTGGACGATTTGGAACCTCCTTGAAAATTGGTAT
TGTTGGATTGCCAAATGTCGGGAAATCTACCTTCTTCAATGTATTAACCAATAGTCAAGCTTCAGCAGAAAACTTCCCAT
TCTGCACTATTGATCTGAATGAGAGCAGAGTACCTGTGCCCGATGAAAGGTCTGACTTTCTTTGCCAGTACCACAAGCCA
GCAAGCAAAATTCCTGCCTTTCTAAATGTAGTGGATATTGCTGGTCTCGTGAAAGGAGCTCACAATGGGCAAGGCCTGGG
AAACGCCTTCTTGTCACATATTAGTGCCTGTGATGGAATCTTTCATCTAACACGTGCTTTTGAAGATGATGATATGAGGC
ATGTTGAAGGAAGTGTAGATCCTATTCGAGATACAGAAATGATACATGAAGAACTTCAGCTTAAAGATGAGGAAATGATT
GGGCCCATTATAGATAAACTAGAAAAAGTGGCTGTGAGAGGAGGAGATAAAAAACCAAAACCTGAATATGACATAATGTG
CAAAGTCAAATCTTGGGTTATAGATCAAAAGAAACCTGTTTGCTTCTATCGTGATTGCAATGACAGAGATTGAAGTGTTG
AATAAACACTTATTTCTGACTTCA

Alignment

ORF - retro_vpac_52 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.34 %
• Parental protein coverage: 55.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPPKKGSDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER
          MPPKKGSDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTID.NESRVPVPDER
Retrocopy MPPKKGSDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDLNESRVPVPDER

Parental  FDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIFHLTRAFEDDDITHVEGSVD
          .DFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIFHLTRAFEDDD..HVEGSVD
Retrocopy SDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIFHLTRAFEDDDMRHVEGSVD

Parental  PIRDIEIIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQKKPVRFYHDWNDKE
          PIRD.E.IHEELQLKDEEMIGPIIDKLEKVAVRGGDKK.KPEYDIMCKVKSWVIDQKKPV.FY.D.ND..
Retrocopy PIRDTEMIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKPKPEYDIMCKVKSWVIDQKKPVCFYRDCNDRD

Parental  -DEVDKHLFLTS
          .....KHLFLTS
Retrocopy >EVLNKHLFLTS

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_52 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_52 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006970	1 retrocopy	retro_btau_1737,
Choloepus hoffmanni	ENSCHOG00000005044	1 retrocopy	retro_chof_1295,
Callithrix jacchus	ENSCJAG00000007877	1 retrocopy	retro_cjac_2875,
Dipodomys ordii	ENSDORG00000008681	1 retrocopy	retro_dord_556,
Homo sapiens	ENSG00000138430	1 retrocopy	retro_hsap_2593,
Gorilla gorilla	ENSGGOG00000022215	1 retrocopy	retro_ggor_1623,
Myotis lucifugus	ENSMLUG00000025196	1 retrocopy	retro_mluc_626,
Monodelphis domestica	ENSMODG00000009296	1 retrocopy	retro_mdom_1428,
Nomascus leucogenys	ENSNLEG00000005817	1 retrocopy	retro_nleu_1526,
Otolemur garnettii	ENSOGAG00000016557	1 retrocopy	retro_ogar_1697,
Pongo abelii	ENSPPYG00000012943	2 retrocopies	retro_pabe_1912, retro_pabe_928,
Pan troglodytes	ENSPTRG00000012650	1 retrocopy	retro_ptro_1517,
Sorex araneus	ENSSARG00000010743	1 retrocopy	retro_sara_545,
Tarsius syrichta	ENSTSYG00000005517	2 retrocopies	retro_tsyr_1845, retro_tsyr_394,
Vicugna pacos	ENSVPAG00000009660	2 retrocopies	retro_vpac_52 , retro_vpac_613,