RetrogeneDB ID: retro_ecab_262

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:23309426..23309929(-)
• Located in intron of: ENSECAG00000019122

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMM17A
• Ensembl ID: ENSECAG00000021816
• Aliases: None
• Description: translocase of inner mitochondrial membrane 17 homolog A (yeast) [Source:HGNC Symbol;Acc:17315]

Sequence

>retro_ecab_262
GAGGAGTATGAGCTAGAGCCGTGCCCTGGTGAACTATGGAAGACCATGATGGGCCTTTACCATGGGAACCATAGGTGGCG
GGGTCTTTCAAGCAATTGAAGGTTTTTGTCATTCTCCAGTAGGAATGAACCAGAGACTACAAGGGAGTTTGACAGCTATT
AACACCAGGTCTCCACAGTTGGGAGGTAGCTTTGCAGTTTGGGGAGGTCTGTGTTCCATGACTGACTGCAGTATGGTTAG
AGAGAACGAAGATCTGTGGAACTCCATCACCAGTCTGCCTCAACAGGAACCACAATGGCAGCAAGAAATGGACGAGTGGC
TATGGTTGTTGGGTCAGCTGTGACGGGTGGCATTCTCCTAGATTTAACTGGAGGAGCTGGTACCTTGTTGACAAGAATTG
CCTTTGCGCACTTTCCCAGTGGTCCTTAGTTTACTGAGACCCCTCCCGGTTGCCTTCAACCCAGTTACCACCCTCACCTT
TTAGAGACTATGGACAATACCAA

Alignment

ORF - retro_ecab_262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.71 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EEYVREPCP-WRIVDDCGG-AFTMGTIGGGIFQAIKGFRNSPVGVNHRLRGSLTAIKTRAPQLGGSFAVW
          EEY..EPCP.W....D..G.AFTMGTIGGG.FQAI.GF..SPVG.N.RL.GSLTAI.TR.PQLGGSFAVW
Retrocopy EEYELEPCP<W*TMEDHDG<AFTMGTIGGGVFQAIEGFCHSPVGMNQRLQGSLTAINTRSPQLGGSFAVW

Parental  GGLFSMIDCSMVQVRGKEDPWNSITS-GALTGAILAARNGPVAM-VGSAAVGGILLALIEGAGILLTRFA
          GGL.SM.DCSM..VR..ED.WNSITS..A.TG...AARNG.VAM.VGSA..GGILL.L..GAG.LLTR.A
Retrocopy GGLCSMTDCSM--VRENEDLWNSITS<SASTGTTMAARNGRVAMVVGSAVTGGILLDLTGGAGTLLTRIA

Parental  SAQFPNGPQFAE-DPSQLPAAQLPSSPFGDYRQYQ
          .A.FP.GP.F.E.DPS.LP..QLP.SPF.DY.QYQ
Retrocopy FAHFPSGP*FTE<DPSRLPSTQLPPSPFRDYGQYQ

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.00 RPM	32.94 RPM
SRP021940_cerebellum	0.00 RPM	31.00 RPM
SRP021940_embryo	0.00 RPM	29.82 RPM
SRP021940_placental_villous	0.00 RPM	25.50 RPM
SRP021940_synovial_membrane	0.08 RPM	22.95 RPM
SRP021940_testis	0.00 RPM	33.12 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_262 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_262 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_262 has 0 orthologous retrocopies within eutheria group .

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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,