RetrogeneDB ID: retro_vpac_322

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_790:318363..319038(-)
• Located in intron of: ENSVPAG00000009366

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS3A
• Ensembl ID: ENSVPAG00000004235
• Aliases: None
• Description: ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]

Sequence

>retro_vpac_322
CTATATTCAATATAAAAAATATTGAAAAAACTAGTCATGAGAACTTAAGGAACCAAAATCACATCTGATGGCCTCAAGAA
TCATGTTTTTGAAGTGTGCTTTGCTGATCTGGAGAATGATGAAGTTGCATTTAGAAAATTCAAGCTAATTACGGAGAATG
TTCAAGGCAAAAACTATCCAAGTAATTTCCATGGCACAGATCTTACCTGTGATAAAATGTGCTGCACGGTAAAAAAAATG
GCAGCCCATGACTGATGCTCATGTTGATGTCAAGACTGCGGGTGGTTATTAGCTCTATCTATTCTGTGTTGGTTTTACTT
AAAAACGCAACAGTCAGATGCAGAAGACCTCACACGCAGCACCAACAGGACTGCCAAATCCAGAAGAAGATGATGAAAAT
TATATCCCAACAGGTACGTACAAATGACTTTAAAAAAGTGGCCAATAAATTGATTTCAGATAGTGTTGGAAAAGACATAG
AAAAGGTATGCCAATCTAGTAATCTGCCCTATCATGACTTTGATAGCAAAGCAAAAATGCTGAATCCCCAAATTTGAATT
GGGAAAATTCGTGTATCATGGCGAAGGCAGTGGTTTTGCAAAAGCTACTGGGGATAAGACAGGTGCTAAAGTTGAACAAG
CTGATGGATATGAGCCACCAGTCCAAAAATCTGTT

Alignment

ORF - retro_vpac_322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.2 %
• Parental protein coverage: 85.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFNIRNVGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTR
          ...I....K.LV.RT.GTKI.SDGLK..VFEV..ADL.NDEVAFRKFKLITE.VQGKN...NFHG.DLT.
Retrocopy LYSI*KILKKLVMRT*GTKITSDGLKNHVFEVCFADLENDEVAFRKFKLITENVQGKNYPSNFHGTDLTC

Parental  DKMC-SMVKKWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYA-QHQQVRQIRKKMMEIMTRE
          DKMC......WQ.M..AHVDVKT..GY.L.LFCVGFT.KRN.Q..KTS.A...Q......K.M..I....
Retrocopy DKMC>ARXXXWQPMTDAHVDVKTAGGY*LYLFCVGFT*KRNSQMQKTSHA>HQQDCQIQKKMM-KIISQQ

Parental  VQTNDLKEVVNKLIPDSIGKDIEKACQSI-YPLHDVFVRKVKMLKKPK-FELGKLMELHGEGSSSGKATG
          V.TND.K.V.NKLI.DS.GKDIEK.CQS...P.HD.F..K.KML..P..FELGK....HGEGS...KATG
Retrocopy VRTNDFKKVANKLISDSVGKDIEKVCQSSNLPYHD-FDSKAKML-NPQ>FELGKFV-YHGEGSGFAKATG

Parental  DETGAKVERADGYEPPVQESV
          D.TGAKVE.ADGYEPPVQ.SV
Retrocopy DKTGAKVEQADGYEPPVQKSV

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_322 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_322 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 13 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018425	11 retrocopies	retro_amel_1333, retro_amel_1361, retro_amel_1380, retro_amel_1514, retro_amel_159, retro_amel_1697, retro_amel_1732, retro_amel_1739, retro_amel_230, retro_amel_367, retro_amel_863,
Bos taurus	ENSBTAG00000009908	3 retrocopies	retro_btau_1284, retro_btau_1733, retro_btau_233,
Canis familiaris	ENSCAFG00000007990	7 retrocopies	retro_cfam_103, retro_cfam_146, retro_cfam_169, retro_cfam_170, retro_cfam_179, retro_cfam_222, retro_cfam_77,
Callithrix jacchus	ENSCJAG00000002268	7 retrocopies	retro_cjac_2, retro_cjac_21, retro_cjac_249, retro_cjac_312, retro_cjac_337, retro_cjac_368, retro_cjac_78,
Gorilla gorilla	ENSGGOG00000003182	2 retrocopies	retro_ggor_70, retro_ggor_97,
Microcebus murinus	ENSMICG00000004921	9 retrocopies	retro_mmur_1230, retro_mmur_1289, retro_mmur_193, retro_mmur_299, retro_mmur_330, retro_mmur_526, retro_mmur_592, retro_mmur_626, retro_mmur_945,
Macaca mulatta	ENSMMUG00000021821	1 retrocopy	retro_mmul_2297,
Monodelphis domestica	ENSMODG00000000969	6 retrocopies	retro_mdom_1040, retro_mdom_1229, retro_mdom_1396, retro_mdom_1480, retro_mdom_627, retro_mdom_694,
Mus musculus	ENSMUSG00000028081	2 retrocopies	retro_mmus_218, retro_mmus_254,
Oryctolagus cuniculus	ENSOCUG00000007011	1 retrocopy	retro_ocun_257,
Rattus norvegicus	ENSRNOG00000011893	1 retrocopy	retro_rnor_198,
Sarcophilus harrisii	ENSSHAG00000015088	2 retrocopies	retro_shar_777, retro_shar_95,
Vicugna pacos	ENSVPAG00000004235	8 retrocopies	retro_vpac_253, retro_vpac_31, retro_vpac_322 , retro_vpac_439, retro_vpac_486, retro_vpac_497, retro_vpac_529, retro_vpac_88,