RetrogeneDB ID: retro_vpac_122

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1939:405785..406284(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HPRT1
• Ensembl ID: ENSVPAG00000009133
• Aliases: None
• Description: hypoxanthine phosphoribosyltransferase 1 [Source:HGNC Symbol;Acc:5157]

Sequence

>retro_vpac_122
CTTGCTCGAGATGTGATGAAGGATATGGGAGGCTATCACGCAGTGGCCCTCTCTGTCCTCAAGGAGAGCTACAAATTCTT
TGCTGACCTGTCGGATTACATTAAAGCACTGAAAAGAAACAGTGAGAGATCCGTTCCTATGCTGTAGATTTTATCAGACT
GAAGAGCAACTGAAATGACCAGTCAATAGGTGATATAAGAGTAATTGGTGGAGACGATCTCTCAACTTTAACTGGAAAGA
ATGTCTTGATTTTTGAAGATATAATTGACACTGGCAAAACAATGCAAACCTTGCTGTCCTTGGTCAGCAGTAAAATACAA
AGATGGTCAAGTTTGCTAGTGAAAAGGACCCCTCAAAATATTGGATACAGACCAGACTTTGTTGGATTTGAAATTTCAGA
TAAGTTTGTCGTAGGATATGTCTTCACTATAATGAATACTTCAGGGATGTGAATCATGTTTGTGTCATTAGTGAAACTGG
AAAAGCCAAAAACAAAGCC

Alignment

ORF - retro_vpac_122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.07 %
• Parental protein coverage: 77.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPM-TVDFIRLKSYCNDQSTGDIKVI
          LARDVMK.MGG.H.VAL.VLK..YKFFADL.DYIKAL.RNS.RS.PM..VDFIRLKS..NDQS.GDI.VI
Retrocopy LARDVMKDMGGYHAVALSVLKESYKFFADLSDYIKALKRNSERSVPM<AVDFIRLKSN*NDQSIGDIRVI

Parental  GGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVKQHNPKMVKVASLLVKRTPRSVGYRPDFVGFEIPDKF
          GGDDLSTLTGKNVLI.EDIIDTGKTMQTLLSLV.....K.....SLLVKRTP...GYRPDFVGFEI.DKF
Retrocopy GGDDLSTLTGKNVLIFEDIIDTGKTMQTLLSLVSS---KIQRWSSLLVKRTPQNIGYRPDFVGFEISDKF

Parental  VVGY-ALDYNEYFRDLNHVCVISETGKAKYKA
          VVGY..L.YNEYFRD.NHVCVISETGKAK.KA
Retrocopy VVGY<CLHYNEYFRDVNHVCVISETGKAKNKA

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_122 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_122 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 21 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001339	1 retrocopy	retro_amel_129,
Bos taurus	ENSBTAG00000014685	3 retrocopies	retro_btau_162, retro_btau_179, retro_btau_721,
Cavia porcellus	ENSCPOG00000002512	1 retrocopy	retro_cpor_1299,
Dasypus novemcinctus	ENSDNOG00000008495	5 retrocopies	retro_dnov_1480, retro_dnov_1908, retro_dnov_2057, retro_dnov_255, retro_dnov_763,
Equus caballus	ENSECAG00000017534	1 retrocopy	retro_ecab_734,
Felis catus	ENSFCAG00000004575	2 retrocopies	retro_fcat_104, retro_fcat_1608,
Homo sapiens	ENSG00000165704	1 retrocopy	retro_hsap_917,
Gorilla gorilla	ENSGGOG00000008050	1 retrocopy	retro_ggor_740,
Loxodonta africana	ENSLAFG00000009892	2 retrocopies	retro_lafr_1042, retro_lafr_475,
Microcebus murinus	ENSMICG00000006547	1 retrocopy	retro_mmur_1186,
Myotis lucifugus	ENSMLUG00000003591	1 retrocopy	retro_mluc_2107,
Macaca mulatta	ENSMMUG00000008303	1 retrocopy	retro_mmul_1118,
Oryctolagus cuniculus	ENSOCUG00000003186	1 retrocopy	retro_ocun_1082,
Otolemur garnettii	ENSOGAG00000003881	3 retrocopies	retro_ogar_1886, retro_ogar_3298, retro_ogar_3463,
Pongo abelii	ENSPPYG00000020733	2 retrocopies	retro_pabe_3601, retro_pabe_791,
Pan troglodytes	ENSPTRG00000022287	2 retrocopies	retro_ptro_2042, retro_ptro_636,
Rattus norvegicus	ENSRNOG00000031367	2 retrocopies	retro_rnor_1208, retro_rnor_2491,
Sarcophilus harrisii	ENSSHAG00000007965	3 retrocopies	retro_shar_470, retro_shar_513, retro_shar_661,
Tupaia belangeri	ENSTBEG00000000859	5 retrocopies	retro_tbel_1607, retro_tbel_2234, retro_tbel_3627, retro_tbel_4320, retro_tbel_729,
Tarsius syrichta	ENSTSYG00000009579	1 retrocopy	retro_tsyr_2050,
Vicugna pacos	ENSVPAG00000009133	1 retrocopy	retro_vpac_122 ,