RetrogeneDB ID: retro_vpac_236

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3140:1297227..1297720(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL12
• Ensembl ID: ENSVPAG00000005123
• Aliases: None
• Description: ribosomal protein L12 [Source:HGNC Symbol;Acc:10302]

Sequence

>retro_vpac_236
ATGCTGCCTAAGTTCAACCCCAGTGAGATTAAAGCCATATACCTGAGATGCACTGCTGGGGAAGTTGGTGCCACACCTGC
CTTGGCCCCCCATATTGGTTCCCTGGGTCTGTTTCCAAAAAGGCTGGTGATGACATAGCCAAGGCCACTGGTGGTTGGAA
GGGTCTGAGGATTACAGTGAGACTGATCATTCAGAACAGACAGGCCCAGACTGACATGGTACCTTCTGCCTCTGCTCTGA
TCATCAAAGCCCTCAAGGAACCACCAAGAGACAGAGAGAAGCAGAAAAATATTAAGCACAGGGGAAACATCACATTTGAT
GAGGCTGTCAACATGGCCTGATAGATGCAGCACTGATCCTTAGCTAGAGGACTCTCTGGAACCATTAAAGAGATCCCGGG
ACTGCCCAGGCTGTGGGTTGCACTGTTGATGGCCACCACTCTCATAATGTCATGGATAACATCAACGGTGGCGTGGTGGA
ATGCCCAGCTAGT

Alignment

ORF - retro_vpac_236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPK-KVGDDIAKATGDWKGLRITVKLTIQNRQA
          M.PKF.P.EIK..YLRCT.GEVGAT.ALAP.IG.LGL.PK.K.GDDIAKATG.WKGLRITV.L.IQNRQA
Retrocopy MLPKFNPSEIKAIYLRCTAGEVGATPALAPHIGSLGLFPK<KAGDDIAKATGGWKGLRITVRLIIQNRQA

Parental  QIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEI-LGTAQS
          Q...VPSASALIIKALKEPPRDR.KQKNIKH.GNITFDE.VN.A..M.H.SLAR.LSGTIKEI..GTAQ.
Retrocopy QTDMVPSASALIIKALKEPPRDREKQKNIKHRGNITFDEAVNMA**MQH*SLARGLSGTIKEI<PGTAQA

Parental  VGCNVDGRHPHDIIEDINSGAVECPAS
          VGC.VDG.H.H.....IN.G.VECPAS
Retrocopy VGCTVDGHHSHNVMDNINGGVVECPAS

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_236 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_236 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 11 parental genes, and 107 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006963	3 retrocopies	retro_btau_102, retro_btau_2, retro_btau_5,
Callithrix jacchus	ENSCJAG00000018082	1 retrocopy	retro_cjac_221,
Latimeria chalumnae	ENSLACG00000015373	3 retrocopies	retro_lcha_31, retro_lcha_87, retro_lcha_92,
Macropus eugenii	ENSMEUG00000007380	12 retrocopies	retro_meug_1102, retro_meug_1107, retro_meug_1199, retro_meug_1357, retro_meug_1426, retro_meug_1611, retro_meug_1634, retro_meug_1691, retro_meug_1953, retro_meug_265, retro_meug_479, retro_meug_493,
Macaca mulatta	ENSMMUG00000000422	2 retrocopies	retro_mmul_1823, retro_mmul_53,
Monodelphis domestica	ENSMODG00000004571	9 retrocopies	retro_mdom_1061, retro_mdom_1177, retro_mdom_1192, retro_mdom_1526, retro_mdom_1719, retro_mdom_1871, retro_mdom_1947, retro_mdom_309, retro_mdom_925,
Mus musculus	ENSMUSG00000038900	1 retrocopy	retro_mmus_28,
Pongo abelii	ENSPPYG00000019622	44 retrocopies	retro_pabe_1009, retro_pabe_1084, retro_pabe_1095, retro_pabe_1127, retro_pabe_1159, retro_pabe_1223, retro_pabe_1246, retro_pabe_1309, retro_pabe_1361, retro_pabe_1471, retro_pabe_1509, retro_pabe_1577, retro_pabe_1659, retro_pabe_1660, retro_pabe_1736, retro_pabe_1794, retro_pabe_1806, retro_pabe_1820, retro_pabe_1969, retro_pabe_1982, retro_pabe_2000, retro_pabe_2149, retro_pabe_2328, retro_pabe_2531, retro_pabe_2802, retro_pabe_2859, retro_pabe_2928, retro_pabe_2947, retro_pabe_3002, retro_pabe_3146, retro_pabe_3185, retro_pabe_3276, retro_pabe_3363, retro_pabe_3405, retro_pabe_3482, retro_pabe_3693, retro_pabe_488, retro_pabe_521, retro_pabe_604, retro_pabe_620, retro_pabe_757, retro_pabe_815, retro_pabe_831, retro_pabe_904,
Pan troglodytes	ENSPTRG00000022808	1 retrocopy	retro_ptro_21,
Rattus norvegicus	ENSRNOG00000016220	4 retrocopies	retro_rnor_166, retro_rnor_236, retro_rnor_247, retro_rnor_312,
Vicugna pacos	ENSVPAG00000005123	27 retrocopies	retro_vpac_158, retro_vpac_181, retro_vpac_189, retro_vpac_191, retro_vpac_194, retro_vpac_236 , retro_vpac_268, retro_vpac_276, retro_vpac_291, retro_vpac_306, retro_vpac_323, retro_vpac_36, retro_vpac_37, retro_vpac_377, retro_vpac_413, retro_vpac_43, retro_vpac_432, retro_vpac_465, retro_vpac_482, retro_vpac_494, retro_vpac_506, retro_vpac_55, retro_vpac_569, retro_vpac_615, retro_vpac_80, retro_vpac_83, retro_vpac_90,