RetrogeneDB ID: retro_pcap_357

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_48387:6858..7304(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPT1
• Ensembl ID: ENSPCAG00000016228
• Aliases: None
• Description: tumor protein, translationally-controlled 1 [Source:HGNC Symbol;Acc:12022]

Sequence

>retro_pcap_357
CTGATGGTCTGCCAGGACCTCCTCAGCTGTGATGAGCTATTCTCCAATATTTATAAGATCCAGGAGATGGTGGCACAGCT
GGAGGTAGAGGGGATGACAGTCCAAGGGACAGACGGTAACACTGATGACTTCCTCCCTGCTGGAGATGCCTCACCAGGAG
GCTCCAATGGTGAAGAGACCTTGGAAAGCACAGTAGACTCTGGTGTTGATATTGTCACCAACCATCACTGCAGAAAATCA
GCTTCAAAAAACAAGCTGAGAAGAAGTACAGCAAAGATTACATGAAATCAGTCAAAGGCAAACTTGAAGAAGAAAGACGA
GAAAGAGTAAACTCTTTTACGATAGGGGCTAAAGAGTGAACCAAATACATCCTTACTAATTTTAAAAACTATCAGCCCTT
TATTGGTGAAGATATGAATCCAGATGGTAAGGTTGCTCTGCTAGAG

Alignment

ORF - retro_pcap_357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.84 %
• Parental protein coverage: 79.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIIYRDLISHDEMFSDIYKIREIADGLCLEVEGKMVSRTEGNIDDSLIGGNASAEGPEGEGT-ESTVITG
          .....DL.S.DE.FS.IYKI.E....L..EVEG..V..T.GN.DD.L..G.AS..G..GE.T.ESTV..G
Retrocopy LMVCQDLLSCDELFSNIYKIQEMVAQL--EVEGMTVQGTDGNTDDFLPAGDASPGGSNGEETLESTVDSG

Parental  VDIVINHH-LQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGE
          VDIV.NHH.LQ..SF.K.A.KKY.KDYMKS.KGKLEE.R.ERV..F..GA.E..K.IL.NFKNYQ.FIGE
Retrocopy VDIVTNHH<LQKISFKKQAEKKYSKDYMKSVKGKLEEERRERVNSFTIGAKE*TKYILTNFKNYQPFIGE

Parental  NMNPDGMVALLD
          .MNPDG.VALL.
Retrocopy DMNPDGKVALLE

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_357 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 25 parental genes, and 163 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006531	2 retrocopies	retro_acar_156, retro_acar_58,
Ailuropoda melanoleuca	ENSAMEG00000013022	8 retrocopies	retro_amel_1153, retro_amel_1521, retro_amel_1593, retro_amel_1804, retro_amel_1878, retro_amel_472, retro_amel_569, retro_amel_969,
Bos taurus	ENSBTAG00000010156	2 retrocopies	retro_btau_21, retro_btau_235,
Canis familiaris	ENSCAFG00000004533	10 retrocopies	retro_cfam_1110, retro_cfam_1328, retro_cfam_1476, retro_cfam_1508, retro_cfam_1846, retro_cfam_254, retro_cfam_341, retro_cfam_483, retro_cfam_661, retro_cfam_777,
Callithrix jacchus	ENSCJAG00000019229	2 retrocopies	retro_cjac_1786, retro_cjac_314,
Cavia porcellus	ENSCPOG00000009278	12 retrocopies	retro_cpor_1053, retro_cpor_1215, retro_cpor_1273, retro_cpor_206, retro_cpor_248, retro_cpor_340, retro_cpor_536, retro_cpor_583, retro_cpor_602, retro_cpor_697, retro_cpor_917, retro_cpor_968,
Dasypus novemcinctus	ENSDNOG00000000653	22 retrocopies	retro_dnov_1071, retro_dnov_1202, retro_dnov_1349, retro_dnov_1705, retro_dnov_2082, retro_dnov_2283, retro_dnov_2305, retro_dnov_237, retro_dnov_2412, retro_dnov_2531, retro_dnov_2687, retro_dnov_276, retro_dnov_342, retro_dnov_397, retro_dnov_417, retro_dnov_453, retro_dnov_71, retro_dnov_847, retro_dnov_870, retro_dnov_909, retro_dnov_934, retro_dnov_981,
Equus caballus	ENSECAG00000018348	3 retrocopies	retro_ecab_337, retro_ecab_686, retro_ecab_727,
Echinops telfairi	ENSETEG00000003091	3 retrocopies	retro_etel_1337, retro_etel_1546, retro_etel_248,
Gorilla gorilla	ENSGGOG00000001684	12 retrocopies	retro_ggor_1561, retro_ggor_1681, retro_ggor_1807, retro_ggor_2045, retro_ggor_2484, retro_ggor_2628, retro_ggor_2652, retro_ggor_2877, retro_ggor_2878, retro_ggor_2980, retro_ggor_584, retro_ggor_855,
Latimeria chalumnae	ENSLACG00000004306	2 retrocopies	retro_lcha_24, retro_lcha_34,
Loxodonta africana	ENSLAFG00000021740	7 retrocopies	retro_lafr_1008, retro_lafr_1195, retro_lafr_1211, retro_lafr_1247, retro_lafr_347, retro_lafr_484, retro_lafr_883,
Myotis lucifugus	ENSMLUG00000017709	1 retrocopy	retro_mluc_1332,
Macaca mulatta	ENSMMUG00000022979	2 retrocopies	retro_mmul_158, retro_mmul_85,
Monodelphis domestica	ENSMODG00000014940	2 retrocopies	retro_mdom_128, retro_mdom_9,
Mustela putorius furo	ENSMPUG00000001640	10 retrocopies	retro_mputfur_1043, retro_mputfur_30, retro_mputfur_364, retro_mputfur_565, retro_mputfur_574, retro_mputfur_582, retro_mputfur_677, retro_mputfur_870, retro_mputfur_960, retro_mputfur_967,
Nomascus leucogenys	ENSNLEG00000002108	8 retrocopies	retro_nleu_1262, retro_nleu_1281, retro_nleu_1637, retro_nleu_2127, retro_nleu_2539, retro_nleu_2540, retro_nleu_368, retro_nleu_9,
Oryctolagus cuniculus	ENSOCUG00000023692	2 retrocopies	retro_ocun_40, retro_ocun_75,
Procavia capensis	ENSPCAG00000016228	3 retrocopies	retro_pcap_245, retro_pcap_351, retro_pcap_357 ,
Pongo abelii	ENSPPYG00000005335	5 retrocopies	retro_pabe_1958, retro_pabe_2626, retro_pabe_2809, retro_pabe_83, retro_pabe_900,
Rattus norvegicus	ENSRNOG00000001049	7 retrocopies	retro_rnor_115, retro_rnor_2464, retro_rnor_2706, retro_rnor_411, retro_rnor_886, retro_rnor_908, retro_rnor_958,
Sarcophilus harrisii	ENSSHAG00000001545	1 retrocopy	retro_shar_227,
Ictidomys tridecemlineatus	ENSSTOG00000006931	7 retrocopies	retro_itri_1192, retro_itri_146, retro_itri_266, retro_itri_325, retro_itri_612, retro_itri_700, retro_itri_999,
Tupaia belangeri	ENSTBEG00000013539	25 retrocopies	retro_tbel_1009, retro_tbel_1556, retro_tbel_1634, retro_tbel_1724, retro_tbel_1725, retro_tbel_2086, retro_tbel_2100, retro_tbel_2265, retro_tbel_2278, retro_tbel_2464, retro_tbel_2550, retro_tbel_2767, retro_tbel_3238, retro_tbel_3354, retro_tbel_3403, retro_tbel_3410, retro_tbel_3592, retro_tbel_3888, retro_tbel_4226, retro_tbel_4400, retro_tbel_4526, retro_tbel_459, retro_tbel_4641, retro_tbel_4733, retro_tbel_830,
Vicugna pacos	ENSVPAG00000008472	5 retrocopies	retro_vpac_1, retro_vpac_101, retro_vpac_159, retro_vpac_539, retro_vpac_552,