RetrogeneDB ID: retro_pcap_344

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_43663:10121..10559(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FTH1
• Ensembl ID: ENSPCAG00000010377
• Aliases: None
• Description: ferritin, heavy polypeptide 1 [Source:HGNC Symbol;Acc:3976]

Sequence

>retro_pcap_344
ACTCCATACCCCTCCCAGATGTGCCAGAATTACAACCAGGACTTAGAGGTCACCATCAACTGTCAGATGAACATGGAATC
TATACCTCTTACTTTGATTTGTCCATGTTTAATTACTTGGTTGTGATGATGTGGCTTTGAAGAATTTTGCCTGGCATTTT
CTTCCTCAGTCTCATGAGGTGAGAGAAAATGCTGAGCAACTGGTGAAGAAGGGAGCCAAAGAGGTGGCCAAATCTTCCTT
CTGAGTGACAAGAAACCAGACTGTGGGGACTGAGAAAGCAAGCTGAATACAAAGGGGTGTGCATTACGCTTGGTAAAAAG
AGTGAATCAGTCATTACTTAAACTGTACAGACTAGCCACTGCCAAAATCAACCCTCATTTGTGTGTCTCTATTGAGATGC
ATTACCTGAATGAGCAGGTAAAATCTGTCAAAGAATTG

Alignment

ORF - retro_pcap_344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.67 %
• Parental protein coverage: 80.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TTFPSQVRQNYSQDSEAAINRQINLE-LYASYVYLSMSYYF-DRDDVALKNFAKYFLHQSHEEREHAEKL
          T..PSQ..QNY.QD.E..IN.Q.N.E..Y.SY..LSM..Y....DDVALKNFA..FL.QSHE.RE.AE.L
Retrocopy TPYPSQMCQNYNQDLEVTINCQMNME<IYTSYFDLSMFNYL<GCDDVALKNFAWHFLPQSHEVRENAEQL

Parental  MKLQ-NQRGGRIFLNDIKKPDRDDWESGLNAMECALFLEKNVNQSLLDLHKLATEKNDPHLCDFIETHYL
          .K....QRGG.IFL...KKPD..D.ES.LN...CAL.L.K.VNQSLL.L..LAT.K..PHLC..IE.HYL
Retrocopy VKKG<SQRGGQIFLLSDKKPDCGD*ESKLNTKGCALRLVKRVNQSLLKLYRLATAKINPHLCVSIEMHYL

Parental  DEQVKSIKQL
          .EQVKS.K.L
Retrocopy NEQVKSVKEL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_344 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis 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 21 parental genes, and 257 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016831	1 retrocopy	retro_amel_115,
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,
Homo sapiens	ENSG00000167996	20 retrocopies	retro_hsap_1243, retro_hsap_139, retro_hsap_1432, retro_hsap_2240, retro_hsap_2351, retro_hsap_2662, retro_hsap_2835, retro_hsap_2985, retro_hsap_2996, retro_hsap_316, retro_hsap_3208, retro_hsap_3293, retro_hsap_3589, retro_hsap_4083, retro_hsap_4232, retro_hsap_4671, retro_hsap_484, retro_hsap_81, retro_hsap_87, retro_hsap_898,
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,
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,
Mus musculus	ENSMUSG00000024661	4 retrocopies	retro_mmus_2856, retro_mmus_3417, retro_mmus_3660, retro_mmus_45,
Nomascus leucogenys	ENSNLEG00000003321	29 retrocopies	retro_nleu_1036, retro_nleu_1157, retro_nleu_136, retro_nleu_1411, retro_nleu_1503, retro_nleu_1532, retro_nleu_1732, retro_nleu_1886, retro_nleu_2049, retro_nleu_2143, retro_nleu_2162, retro_nleu_2163, retro_nleu_2281, retro_nleu_2356, retro_nleu_2357, retro_nleu_2358, retro_nleu_2359, retro_nleu_2360, retro_nleu_2361, retro_nleu_2417, retro_nleu_2433, retro_nleu_2962, retro_nleu_303, retro_nleu_383, retro_nleu_72, retro_nleu_738, retro_nleu_747, retro_nleu_78, retro_nleu_936,
Oryctolagus cuniculus	ENSOCUG00000014108	4 retrocopies	retro_ocun_1172, retro_ocun_1179, retro_ocun_1598, retro_ocun_93,
Procavia capensis	ENSPCAG00000010377	13 retrocopies	retro_pcap_177, retro_pcap_217, retro_pcap_248, retro_pcap_276, retro_pcap_344 , retro_pcap_348, retro_pcap_374, retro_pcap_379, retro_pcap_383, retro_pcap_395, retro_pcap_447, retro_pcap_5, retro_pcap_62,
Procavia capensis	ENSPCAG00000013227	6 retrocopies	retro_pcap_120, retro_pcap_156, retro_pcap_258, retro_pcap_376, retro_pcap_384, retro_pcap_85,
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,
Rattus norvegicus	ENSRNOG00000022619	9 retrocopies	retro_rnor_1197, retro_rnor_1280, retro_rnor_1356, retro_rnor_1832, retro_rnor_2060, retro_rnor_2163, retro_rnor_264, retro_rnor_427, retro_rnor_71,
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,