RetrogeneDB ID: retro_vpac_105

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1838:422391..422760(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5G2
• Ensembl ID: ENSVPAG00000000409
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9) [Source:HGNC Symbol;Acc:842]

Sequence

>retro_vpac_105
GTCAGGAGCACCCCTGAGCTGCCAAGCCGACCAGTGTCTGCAGTAGTGATGAAACAACTAAAGATGCTGACAAGTGAGAA
CCTTAGCAACTTGCCAGCCTTAGCGCCCTTGACCTCACTTATGCTTAAGACATAACTTCCAACCCAGTGCCATTTCAGAG
ACATTGATAGAGCAGCCAAGTTCACTGGGGCTGTGCCTGCCCCAGTTGGGATGGCTAGCTCTGGGGTGGGTTTGGGAGCC
ATTATTGGCTATGCCAGAAACTCTTCTCTGAAGCAACAGCTCTTCTCCTGTGCCGTTCTGGGCTTTGCCCTCTTTGAGGC
TATGGGGCTCTTTCCCCTGATTGTAGTCTTTTCTATTCTCTTTGCCATG

Alignment

ORF - retro_vpac_105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.31 %
• Parental protein coverage: 64.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IRRTSPLLSRSLSAVVLKQPETLTDESHSSLAAARPLTTSLIPS-RGFQTSAVS-RDIDTAAKFIGAGAA
          .R.T..L.SR..SAVV.KQ...LT.E..S.L.A..PL.TSL......FQ.SA.S.RDID.AAKF.GA..A
Retrocopy VRSTPELPSRPVSAVVMKQLKMLTSENLSNLPALAPL-TSLMLK>HNFQPSAIS<RDIDRAAKFTGAVPA

Parental  TVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM
          .VG.A.S..G.G......IIGYARN.SLKQQLFS.A.LGFAL.EAMGLF.L.V.F.ILFAM
Retrocopy PVGMASS--GVGL---GAIIGYARNSSLKQQLFSCAVLGFALFEAMGLFPLIVVFSILFAM

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_105 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_105 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 18 parental genes, and 177 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022889	3 retrocopies	retro_cpor_1495, retro_cpor_268, retro_cpor_492,
Dipodomys ordii	ENSDORG00000002955	1 retrocopy	retro_dord_610,
Echinops telfairi	ENSETEG00000005968	40 retrocopies	retro_etel_1001, retro_etel_1007, retro_etel_103, retro_etel_1191, retro_etel_1203, retro_etel_1259, retro_etel_1288, retro_etel_1301, retro_etel_1327, retro_etel_1332, retro_etel_1354, retro_etel_1374, retro_etel_1402, retro_etel_1404, retro_etel_1420, retro_etel_1427, retro_etel_144, retro_etel_1533, retro_etel_1535, retro_etel_1591, retro_etel_1662, retro_etel_1684, retro_etel_1712, retro_etel_1771, retro_etel_2011, retro_etel_2127, retro_etel_2128, retro_etel_2142, retro_etel_2207, retro_etel_2216, retro_etel_260, retro_etel_475, retro_etel_636, retro_etel_639, retro_etel_652, retro_etel_72, retro_etel_735, retro_etel_736, retro_etel_796, retro_etel_847,
Felis catus	ENSFCAG00000001502	13 retrocopies	retro_fcat_1126, retro_fcat_1345, retro_fcat_1611, retro_fcat_1785, retro_fcat_1952, retro_fcat_226, retro_fcat_351, retro_fcat_353, retro_fcat_363, retro_fcat_405, retro_fcat_668, retro_fcat_958, retro_fcat_999,
Gorilla gorilla	ENSGGOG00000015641	5 retrocopies	retro_ggor_1039, retro_ggor_1737, retro_ggor_1884, retro_ggor_2543, retro_ggor_2999,
Macropus eugenii	ENSMEUG00000004661	67 retrocopies	retro_meug_1009, retro_meug_1030, retro_meug_113, retro_meug_1180, retro_meug_1187, retro_meug_1238, retro_meug_1258, retro_meug_1261, retro_meug_1265, retro_meug_1272, retro_meug_1284, retro_meug_1297, retro_meug_1322, retro_meug_1328, retro_meug_1361, retro_meug_1389, retro_meug_1413, retro_meug_1602, retro_meug_1626, retro_meug_1639, retro_meug_1653, retro_meug_1709, retro_meug_1752, retro_meug_177, retro_meug_1802, retro_meug_1843, retro_meug_1882, retro_meug_1885, retro_meug_1891, retro_meug_1903, retro_meug_1909, retro_meug_1919, retro_meug_193, retro_meug_1987, retro_meug_2014, retro_meug_2048, retro_meug_206, retro_meug_2073, retro_meug_2111, retro_meug_2115, retro_meug_2122, retro_meug_216, retro_meug_229, retro_meug_230, retro_meug_296, retro_meug_313, retro_meug_345, retro_meug_348, retro_meug_397, retro_meug_485, retro_meug_514, retro_meug_529, retro_meug_567, retro_meug_622, retro_meug_66, retro_meug_721, retro_meug_742, retro_meug_799, retro_meug_800, retro_meug_846, retro_meug_864, retro_meug_865, retro_meug_896, retro_meug_904, retro_meug_935, retro_meug_936, retro_meug_983,
Myotis lucifugus	ENSMLUG00000011860	13 retrocopies	retro_mluc_106, retro_mluc_1215, retro_mluc_1335, retro_mluc_1337, retro_mluc_1496, retro_mluc_1633, retro_mluc_2151, retro_mluc_2186, retro_mluc_2257, retro_mluc_2273, retro_mluc_516, retro_mluc_575, retro_mluc_656,
Macaca mulatta	ENSMMUG00000016241	3 retrocopies	retro_mmul_1539, retro_mmul_2173, retro_mmul_439,
Mustela putorius furo	ENSMPUG00000005927	6 retrocopies	retro_mputfur_1650, retro_mputfur_290, retro_mputfur_335, retro_mputfur_631, retro_mputfur_814, retro_mputfur_947,
Mus musculus	ENSMUSG00000062683	1 retrocopy	retro_mmus_6,
Oryctolagus cuniculus	ENSOCUG00000008933	4 retrocopies	retro_ocun_1933, retro_ocun_450, retro_ocun_762, retro_ocun_794,
Otolemur garnettii	ENSOGAG00000003611	4 retrocopies	retro_ogar_142, retro_ogar_1620, retro_ogar_166, retro_ogar_2415,
Ochotona princeps	ENSOPRG00000002978	1 retrocopy	retro_opri_671,
Procavia capensis	ENSPCAG00000008679	3 retrocopies	retro_pcap_140, retro_pcap_189, retro_pcap_212,
Sorex araneus	ENSSARG00000001027	7 retrocopies	retro_sara_124, retro_sara_152, retro_sara_377, retro_sara_581, retro_sara_716, retro_sara_73, retro_sara_759,
Sarcophilus harrisii	ENSSHAG00000005726	4 retrocopies	retro_shar_163, retro_shar_417, retro_shar_653, retro_shar_678,
Vicugna pacos	ENSVPAG00000000409	1 retrocopy	retro_vpac_105 ,
Vicugna pacos	ENSVPAG00000007653	1 retrocopy	retro_vpac_282,