RetrogeneDB ID: retro_dord_160

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_4078:24444..24934(+)
• Located in intron of: ENSDORG00000005887

Retrocopy information

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

Parental gene information

• Parental gene symbol: Timm17a
• Ensembl ID: ENSDORG00000013467
• Aliases: None
• Description: translocase of inner mitochondrial membrane 17a [Source:MGI Symbol;Acc:MGI:1343131]

Sequence

>retro_dord_160
ATGGAGGAGTATGCCTGAGAGCCTTGCTTTGGAGAATTGTGGATGCCTGCGATGGGATCTTCACACAGGTATCATAGGTG
GGCAGCATCATCCAAGCCATCAACGCTTTTCTCATTCTCCCATGGGTGTGAATCACAGATGATGAGGGAGTTTGATGGCT
GTTAAAACCCCAGCTCCCCAGTTGGGAGGTAGCTTTGCTATTGGGGATGGTCTGTTCTCCATGACTGACTGTAGGATGGT
TCAAGTCAGAGGAAAAGAAGATTCCCTGGGACTCCATCACAGGAGCCATCCTGGCAGCCAGAAATGGACAGGCGGCCATG
GTTAGGTCAGCAGCCATGGGAAGCGTTCTCCTAGCTTGAATCGAAGGAGCTGGCATCTTGACAAGGTTTGCCTCTGCAGT
TTCCCAATGCCCTCAGTTTGCTGAAGACCCCTCCCACTTGCCTGCAAGCCAGTTACCTCCTCACTTTTTGGAGACGATCA
ACAATAGCAA

Alignment

ORF - retro_dord_160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEEYAREPC-PWRIVDDCGGAFTMGTIGGGIFQAIKGF-RNSPVGVNHRLRGSLTAIKTRAPQLGGSFAI
          MEEYA.EPC..WRIVD.C.G.FT.....G.I.QAI..F...SP.GVNHR..GSL.A.KT.APQLGGSFAI
Retrocopy MEEYA*EPC<LWRIVDACDGIFTQVS*VGSIIQAINAF<SHSPMGVNHR**GSLMAVKTPAPQLGGSFAI

Parental  WGGLFSMIDCSMVQVRGKED-PWNSITSGALTGAILAARNGPVAMVGSAAMGGILLALIEGAGILLTRFA
          ..GLFSM.DC.MVQVRGKED.PW.SIT.GA...A....RNG..AMV.SAAMG..LLA.IEGAGI.LTRFA
Retrocopy GDGLFSMTDCRMVQVRGKED>PWDSIT-GAILAA----RNGQAAMVRSAAMGSVLLA*IEGAGI-LTRFA

Parental  SAQFPNGPQFAEDPSQLPASQLP-SSPFGDYRQYQ
          SA.....PQFAEDPS.LPASQLP.SS.FGD..Q.Q
Retrocopy SA-VSQCPQFAEDPSHLPASQLP<SSLFGDDQQ*Q

Legend:

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

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_160 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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 26 parental genes, and 76 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012030	4 retrocopies	retro_amel_1667, retro_amel_554, retro_amel_597, retro_amel_622,
Bos taurus	ENSBTAG00000047059	3 retrocopies	retro_btau_1098, retro_btau_1590, retro_btau_872,
Canis familiaris	ENSCAFG00000010612	1 retrocopy	retro_cfam_646,
Choloepus hoffmanni	ENSCHOG00000007440	7 retrocopies	retro_chof_1346, retro_chof_1452, retro_chof_1693, retro_chof_1824, retro_chof_1849, retro_chof_375, retro_chof_435,
Callithrix jacchus	ENSCJAG00000005709	1 retrocopy	retro_cjac_1651,
Dasypus novemcinctus	ENSDNOG00000006389	7 retrocopies	retro_dnov_1113, retro_dnov_1420, retro_dnov_1806, retro_dnov_2586, retro_dnov_273, retro_dnov_274, retro_dnov_814,
Dipodomys ordii	ENSDORG00000013467	4 retrocopies	retro_dord_160 , retro_dord_170, retro_dord_536, retro_dord_76,
Equus caballus	ENSECAG00000021816	6 retrocopies	retro_ecab_1036, retro_ecab_1044, retro_ecab_262, retro_ecab_611, retro_ecab_901, retro_ecab_909,
Echinops telfairi	ENSETEG00000006334	6 retrocopies	retro_etel_1179, retro_etel_1356, retro_etel_1809, retro_etel_1958, retro_etel_2211, retro_etel_820,
Homo sapiens	ENSG00000134375	1 retrocopy	retro_hsap_279,
Loxodonta africana	ENSLAFG00000017314	1 retrocopy	retro_lafr_724,
Myotis lucifugus	ENSMLUG00000006569	1 retrocopy	retro_mluc_585,
Macaca mulatta	ENSMMUG00000001924	1 retrocopy	retro_mmul_562,
Monodelphis domestica	ENSMODG00000000517	2 retrocopies	retro_mdom_1007, retro_mdom_381,
Mustela putorius furo	ENSMPUG00000010908	3 retrocopies	retro_mputfur_1455, retro_mputfur_318, retro_mputfur_598,
Mus musculus	ENSMUSG00000062580	1 retrocopy	retro_mmus_3045,
Nomascus leucogenys	ENSNLEG00000018089	1 retrocopy	retro_nleu_1490,
Oryctolagus cuniculus	ENSOCUG00000007498	3 retrocopies	retro_ocun_1293, retro_ocun_493, retro_ocun_651,
Otolemur garnettii	ENSOGAG00000006176	1 retrocopy	retro_ogar_77,
Pongo abelii	ENSPPYG00000000356	1 retrocopy	retro_pabe_390,
Pan troglodytes	ENSPTRG00000001842	2 retrocopies	retro_ptro_232, retro_ptro_671,
Rattus norvegicus	ENSRNOG00000007040	1 retrocopy	retro_rnor_1417,
Sorex araneus	ENSSARG00000008807	1 retrocopy	retro_sara_270,
Tupaia belangeri	ENSTBEG00000010939	7 retrocopies	retro_tbel_1882, retro_tbel_2869, retro_tbel_2940, retro_tbel_3759, retro_tbel_4197, retro_tbel_4387, retro_tbel_749,
Tarsius syrichta	ENSTSYG00000011606	6 retrocopies	retro_tsyr_1396, retro_tsyr_1512, retro_tsyr_1631, retro_tsyr_1777, retro_tsyr_1920, retro_tsyr_447,
Tursiops truncatus	ENSTTRG00000005973	4 retrocopies	retro_ttru_1044, retro_ttru_1527, retro_ttru_197, retro_ttru_368,