RetrogeneDB ID: retro_vpac_56

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1311:404889..405339(-)
• Located in intron of: ENSVPAG00000002184

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS23
• Ensembl ID: ENSVPAG00000009427
• Aliases: None
• Description: ribosomal protein S23 [Source:HGNC Symbol;Acc:10410]

Sequence

>retro_vpac_56
TTTGCTCACACCCATGGCCCCAGCAGGATGGGCAAGTTTTGGGGGCTTCATACTGCCAGGAAGCTCCATAGCCACTGACA
AGAGCAGATGTGGCATGGTCACTGGTACCAGAAAGCCCATTTGTGCCCAGCCCTGAAGGCCAACCCTTTTGGAGGCACTT
CTCATGCAAAGGTCTTGCTTGTAAAAGTAGAAATTGAAGCCAAGCAGCCAAGTTCTGCCATCAGGAAGTGTGTTAGGATT
CAGCTAATCAAGAATGCCCCCCTACCCCCAAACACAGCCTTTATATCCAATGATGGTTGTTTGGGTTTTACTGAGGAAAA
TGATGAAGTTCTGGTTGCTGGGTTTGGTCACAAAGGTCATGCCGTTGGTGACATTCCCGGAGTTTGCTTTAAGGTTGTTA
AAGTAGCCAGTGTCTCTTGGCTTTATACAAAGGCAAGAAGGAAAGACCAA

Alignment

ORF - retro_vpac_56 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.89 %
• Parental protein coverage: 85.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FAQARGAGRMGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQ
          FA...G..RMGK..GL.TARKL.SH...Q.WH...Y.KAHL..ALKANPFGG.SHAK...L.KV..EAKQ
Retrocopy FAHTHGPSRMGKFWGLHTARKLHSH*QEQMWHGHWYQKAHLCPALKANPFGGTSHAK-VLLVKVEIEAKQ

Parental  PNSAIRKCVRVQLIKNGK--KITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVS
          P.SAIRKCVR.QLIKN......TAF..NDGCL.F.EENDEVLVAGFG.KGHAVGDIPGV.FKVVKVA.VS
Retrocopy PSSAIRKCVRIQLIKNAPLPPNTAFISNDGCLGFTEENDEVLVAGFGHKGHAVGDIPGVCFKVVKVASVS

Parental  LLALYKGKKER
          .L......K..
Retrocopy WLYTKARRKDQ

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_56 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_56 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 19 parental genes, and 80 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015966	3 retrocopies	retro_amel_1096, retro_amel_341, retro_amel_751,
Bos taurus	ENSBTAG00000013358	3 retrocopies	retro_btau_173, retro_btau_205, retro_btau_80,
Canis familiaris	ENSCAFG00000030896	7 retrocopies	retro_cfam_1145, retro_cfam_1305, retro_cfam_1415, retro_cfam_1743, retro_cfam_2105, retro_cfam_375, retro_cfam_436,
Callithrix jacchus	ENSCJAG00000011247	2 retrocopies	retro_cjac_126, retro_cjac_256,
Cavia porcellus	ENSCPOG00000022705	2 retrocopies	retro_cpor_1182, retro_cpor_1377,
Dipodomys ordii	ENSDORG00000001813	2 retrocopies	retro_dord_187, retro_dord_93,
Felis catus	ENSFCAG00000008839	7 retrocopies	retro_fcat_1557, retro_fcat_1601, retro_fcat_1876, retro_fcat_2000, retro_fcat_5, retro_fcat_609, retro_fcat_644,
Macropus eugenii	ENSMEUG00000012931	1 retrocopy	retro_meug_811,
Myotis lucifugus	ENSMLUG00000013939	2 retrocopies	retro_mluc_1676, retro_mluc_2183,
Macaca mulatta	ENSMMUG00000003578	4 retrocopies	retro_mmul_1239, retro_mmul_1974, retro_mmul_2305, retro_mmul_852,
Mustela putorius furo	ENSMPUG00000008114	1 retrocopy	retro_mputfur_1298,
Oryctolagus cuniculus	ENSOCUG00000010363	2 retrocopies	retro_ocun_195, retro_ocun_95,
Otolemur garnettii	ENSOGAG00000008163	11 retrocopies	retro_ogar_1177, retro_ogar_1303, retro_ogar_1785, retro_ogar_1849, retro_ogar_238, retro_ogar_2479, retro_ogar_253, retro_ogar_2695, retro_ogar_2823, retro_ogar_3519, retro_ogar_364,
Pongo abelii	ENSPPYG00000015608	7 retrocopies	retro_pabe_1538, retro_pabe_1585, retro_pabe_19, retro_pabe_2515, retro_pabe_2567, retro_pabe_2716, retro_pabe_3129,
Pteropus vampyrus	ENSPVAG00000002083	4 retrocopies	retro_pvam_1483, retro_pvam_782, retro_pvam_80, retro_pvam_922,
Rattus norvegicus	ENSRNOG00000016580	12 retrocopies	retro_rnor_100, retro_rnor_1394, retro_rnor_149, retro_rnor_1691, retro_rnor_1941, retro_rnor_1959, retro_rnor_1982, retro_rnor_2119, retro_rnor_2182, retro_rnor_2492, retro_rnor_525, retro_rnor_559,
Sarcophilus harrisii	ENSSHAG00000008347	2 retrocopies	retro_shar_257, retro_shar_348,
Sus scrofa	ENSSSCG00000014133	1 retrocopy	retro_sscr_92,
Vicugna pacos	ENSVPAG00000009427	7 retrocopies	retro_vpac_195, retro_vpac_239, retro_vpac_393, retro_vpac_543, retro_vpac_56 , retro_vpac_598, retro_vpac_81,