RetrogeneDB ID: retro_vpac_233

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3081:41830..42349(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000005713
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FTH1
• Ensembl ID: ENSVPAG00000003956
• Aliases: None
• Description: ferritin, heavy polypeptide 1 [Source:HGNC Symbol;Acc:3976]

Sequence

>retro_vpac_233
CAGAACTTCCACCCGGACTCCGAGGCCGCCATCAACCGCCAGATCAATCTGGAGCTCTACGCGTCCTACGTGTACTTGTC
CATGGCCTATTACTTCTCCCGAGACGACGTGGCCTTGCACAACTTCGCCAGGTATTTCCTCCGACAGTCCAGGGAGGAGA
CTGTGCACGCGGAGAAGCTGATGAGGCTGCAGAACCAGCGGGGAGGACGGATCTGCCTTCAGGACATCAAGAAACCAGAA
CAGGATGACTGGGAAAGTGGGCTGAATGCCATGGAGTGTTCATGCTTTTGGAAAAGAATGTGAACCAGTCGTTGCTGGAA
TTGCACACTTTGGCTTCAGACAAAGGCGACCCCCCATTTGTGCGATTTCCTGGAAACCCACTATGTAAATGAGCAGGTGA
AGTCTATCAAAGAATTAGCTGACCTCGTGCACAACTTGGTTAAGATGTGGGCCCCGGATTCTGGCTTAGCGGAGTACCTT
TCTGACAAACATACCCTTGGAAGTGAAAACAATCAGAAC

Alignment

ORF - retro_vpac_233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QNYHQDSKAAINRQIT-QKYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGR
          QN.H.DS.AAINRQI....YASYVYLSM.YYF.RDDVAL.NFA.YFL.QS.EE..HAEKLM.LQNQRGGR
Retrocopy QNFHPDSEAAINRQINLELYASYVYLSMAYYFSRDDVALHNFARYFLRQSREETVHAEKLMRLQNQRGGR

Parental  IFLQDIKKPDYDDWENGLNAMECA-LHLEKSVNQSLLELHKLATDKND-PHLCDFLETHYLNEQVKSIKE
          I.LQDIKKP..DDWE.GLNAMEC....LEK.VNQSLLELH.LA.DK.D.PHLCDFLETHY.NEQVKSIKE
Retrocopy ICLQDIKKPEQDDWESGLNAMECS<MLLEKNVNQSLLELHTLASDKGD>PHLCDFLETHYVNEQVKSIKE

Parental  LGDHVTNLRKMGAPESGIAEFLFDKHTLGNSDNES
          L.D.V.NL.KM.AP.SG.AE.L.DKHTLG...N..
Retrocopy LADLVHNLVKMWAPDSGLAEYLSDKHTLGSENNQN

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_233 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_233 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 202 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015901	1 retrocopy	retro_cfam_150,
Callithrix jacchus	ENSCJAG00000019089	16 retrocopies	retro_cjac_1570, retro_cjac_1634, retro_cjac_2115, retro_cjac_2233, retro_cjac_230, retro_cjac_232, retro_cjac_2320, retro_cjac_2531, retro_cjac_278, retro_cjac_2843, retro_cjac_2857, retro_cjac_485, retro_cjac_519, retro_cjac_699, retro_cjac_767, retro_cjac_804,
Cavia porcellus	ENSCPOG00000026586	3 retrocopies	retro_cpor_1309, retro_cpor_15, retro_cpor_157,
Dasypus novemcinctus	ENSDNOG00000017128	83 retrocopies	retro_dnov_1017, retro_dnov_1074, retro_dnov_1078, retro_dnov_110, retro_dnov_1179, retro_dnov_1188, retro_dnov_1196, retro_dnov_1201, retro_dnov_1205, retro_dnov_1271, retro_dnov_1352, retro_dnov_1356, retro_dnov_1369, retro_dnov_1397, retro_dnov_1415, retro_dnov_1425, retro_dnov_1446, retro_dnov_1489, retro_dnov_1526, retro_dnov_1535, retro_dnov_1554, retro_dnov_1565, retro_dnov_162, retro_dnov_1627, retro_dnov_1640, retro_dnov_1777, retro_dnov_1787, retro_dnov_1792, retro_dnov_1827, retro_dnov_1851, retro_dnov_1865, retro_dnov_1875, retro_dnov_189, retro_dnov_197, retro_dnov_2005, retro_dnov_2065, retro_dnov_2093, retro_dnov_2097, retro_dnov_2109, retro_dnov_2124, retro_dnov_2136, retro_dnov_2154, retro_dnov_2173, retro_dnov_220, retro_dnov_2216, retro_dnov_2231, retro_dnov_2241, retro_dnov_2251, retro_dnov_2356, retro_dnov_2388, retro_dnov_2399, retro_dnov_242, retro_dnov_2443, retro_dnov_2444, retro_dnov_2454, retro_dnov_2476, retro_dnov_2483, retro_dnov_2489, retro_dnov_2511, retro_dnov_2528, retro_dnov_2554, retro_dnov_2579, retro_dnov_2607, retro_dnov_2626, retro_dnov_2646, retro_dnov_304, retro_dnov_383, retro_dnov_409, retro_dnov_422, retro_dnov_471, retro_dnov_517, retro_dnov_52, retro_dnov_55, retro_dnov_589, retro_dnov_61, retro_dnov_661, retro_dnov_675, retro_dnov_722, retro_dnov_726, retro_dnov_810, retro_dnov_864, retro_dnov_890, retro_dnov_994,
Felis catus	ENSFCAG00000007382	1 retrocopy	retro_fcat_887,
Gorilla gorilla	ENSGGOG00000027722	7 retrocopies	retro_ggor_1313, retro_ggor_153, retro_ggor_1671, retro_ggor_1858, retro_ggor_2835, retro_ggor_64, retro_ggor_726,
Latimeria chalumnae	ENSLACG00000017426	1 retrocopy	retro_lcha_75,
Loxodonta africana	ENSLAFG00000004824	12 retrocopies	retro_lafr_106, retro_lafr_1080, retro_lafr_1129, retro_lafr_138, retro_lafr_321, retro_lafr_433, retro_lafr_523, retro_lafr_53, retro_lafr_624, retro_lafr_717, retro_lafr_760, retro_lafr_966,
Microcebus murinus	ENSMICG00000005851	6 retrocopies	retro_mmur_1227, retro_mmur_1303, retro_mmur_1370, retro_mmur_1609, retro_mmur_392, retro_mmur_509,
Myotis lucifugus	ENSMLUG00000025726	16 retrocopies	retro_mluc_1030, retro_mluc_1142, retro_mluc_1211, retro_mluc_1354, retro_mluc_1464, retro_mluc_1769, retro_mluc_1984, retro_mluc_2002, retro_mluc_2091, retro_mluc_212, retro_mluc_2635, retro_mluc_361, retro_mluc_532, retro_mluc_556, retro_mluc_850, retro_mluc_885,
Monodelphis domestica	ENSMODG00000007582	9 retrocopies	retro_mdom_1134, retro_mdom_122, retro_mdom_1294, retro_mdom_1407, retro_mdom_1742, retro_mdom_300, retro_mdom_564, retro_mdom_643, retro_mdom_809,
Mustela putorius furo	ENSMPUG00000014030	3 retrocopies	retro_mputfur_1642, retro_mputfur_36, retro_mputfur_408,
Oryctolagus cuniculus	ENSOCUG00000014108	4 retrocopies	retro_ocun_1172, retro_ocun_1179, retro_ocun_1598, retro_ocun_93,
Otolemur garnettii	ENSOGAG00000025354	9 retrocopies	retro_ogar_1065, retro_ogar_1198, retro_ogar_1518, retro_ogar_2010, retro_ogar_2099, retro_ogar_2349, retro_ogar_2661, retro_ogar_2747, retro_ogar_3380,
Pongo abelii	ENSPPYG00000003173	12 retrocopies	retro_pabe_1034, retro_pabe_1186, retro_pabe_2410, retro_pabe_2483, retro_pabe_2484, retro_pabe_249, retro_pabe_3351, retro_pabe_3406, retro_pabe_35, retro_pabe_3713, retro_pabe_47, retro_pabe_479,
Sus scrofa	ENSSSCG00000014540	9 retrocopies	retro_sscr_1045, retro_sscr_168, retro_sscr_286, retro_sscr_359, retro_sscr_498, retro_sscr_581, retro_sscr_78, retro_sscr_906, retro_sscr_949,
Ictidomys tridecemlineatus	ENSSTOG00000014521	1 retrocopy	retro_itri_250,
Vicugna pacos	ENSVPAG00000003956	6 retrocopies	retro_vpac_233 , retro_vpac_300, retro_vpac_370, retro_vpac_505, retro_vpac_515, retro_vpac_643,
Vicugna pacos	ENSVPAG00000005509	3 retrocopies	retro_vpac_119, retro_vpac_206, retro_vpac_258,