RetrogeneDB ID: retro_ecab_390

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:6692888..6693735(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM3
• Ensembl ID: ENSECAG00000010942
• Aliases: None
• Description: tropomyosin 3 [Source:HGNC Symbol;Acc:12012]

Sequence

>retro_ecab_390
ATGGACGCCATCAAGAAGAAGATGCAGATGCTGGAGCTCAACAAGGAGAATGCCTAGGATTGAGTGGAGCAGGCGGAGGC
CGATAAGGCGGAGGAGGACAGGAGCAAACAGTTGGAAGATGAGCTAGCGTTGCTGCAAAAGAAACTCAAGACCACCAAGA
TGAACTTGACAAATACTCAGAGGCTCTCAGAGATGCCCAGGAGAAGCTGGAGCCGGCAGAGCAAAAGGCCACCGACGCCG
AAGCCAATGCGGCCTCTCTGAACAGATGCATCCAACTGCTTGAGGAAGAGCTGGGTCATGCCCAGGAGTGTCTGGCAACA
GCTCTGCAGAAGCTGGAGGAGGCCAAGAAGGCAGCAGATGAGAGGGAGAGAGGCATGAATGTCATTGAGAGCCGAACCGA
AAAGGATGAAAAGAAAATGGAAATTCAGGAGATCCAACTGTAAGAGGCTAAGCACATGGCTGAAGATGCCAACCGCAATA
TGAAGAGGTGGCCCGTAGGCTGGGCCTTATTGACAGTGACTCGGAATGTGCAGAGGAGTGGGCTGAGCTCACAGATGGCC
AAGTTCGACAGCTGGAAGAACAATTAAGAATAATGGACCAGACCTTGAAAGTGTTAATGGTTGCAGAAGGTAAGTACTCG
CAGAAGGAAGACAAATATGAGGAAGAGATCAAAGTCCTTTCTGACAAGCTGAGGGAGGCTGAGACTCGGGCTGAATTTGC
AAAGAGGTCAGTAATTAAATTGGAGAAAAGCACTGATGACTTAGAAGAGGAGCTGAACGCTCAGAAACTGAAGTACAAAG
CCATCAGCCAGGAGCTGGACCACGCTCTCAACAATGTGATTTCCATG

Alignment

ORF - retro_ecab_390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.63 %
• Parental protein coverage: 99.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEAIKKKMQMLKLDKENALDRAEQAEAEQKQAEERSKQLEDELAAMQKKLKGT-EDELDKYSEALKDAQE
          M.AIKKKMQML.L.KENA.D..EQAEA..K..E.RSKQLEDELA..QKKLK.T..DELDKYSEAL.DAQE
Retrocopy MDAIKKKMQMLELNKENA*D*VEQAEAD-KAEEDRSKQLEDELALLQKKLKTT<QDELDKYSEALRDAQE

Parental  KLELAEKKAADAEAEVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIENRALKDEE
          KLE.AE.KA.DAEA..ASLNR.IQL.EEEL..AQE.LATALQKLEEA.KAADE.ERGM.VIE.R..KDE.
Retrocopy KLEPAEQKATDAEANAASLNRCIQLLEEELGHAQECLATALQKLEEAKKAADERERGMNVIESRTEKDEK

Parental  KMELQEIQLKEAKHIAEEADR-KYEEVARKLVIIEGDLERTEERAELAESKCSELEEELKNVTNNLKSLE
          KME.QEIQL.EAKH.AE.A.R..YEEVAR.L..I..D.E..EE.AEL.......LEE.L......LK.L.
Retrocopy KMEIQEIQL*EAKHMAEDANR<QYEEVARRLGLIDSDSECAEEWAELTDGQVRQLEEQLRIMDQTLKVLM

Parental  AQAEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSVAKLEKTIDDLEDELYAQKLKYKAISEELDHAL
          ....KYSQKEDKYEEEIK.L.DKL.EAETRAEFA.RSV.KLEK..DDLE.EL.AQKLKYKAIS.ELDHAL
Retrocopy VAEGKYSQKEDKYEEEIKVLSDKLREAETRAEFAKRSVIKLEKSTDDLEEELNAQKLKYKAISQELDHAL

Parental  NDMTSI
          N...S.
Retrocopy NNVISM

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	20.01 RPM
SRP021940_cerebellum	0.10 RPM	19.89 RPM
SRP021940_embryo	9.87 RPM	53.24 RPM
SRP021940_placental_villous	4.52 RPM	31.46 RPM
SRP021940_synovial_membrane	3.82 RPM	41.43 RPM
SRP021940_testis	0.26 RPM	24.49 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_390 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_390 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_390 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011877	2 retrocopies	retro_amel_1017, retro_amel_1212,
Bos taurus	ENSBTAG00000033217	3 retrocopies	retro_btau_1166, retro_btau_210, retro_btau_933,
Canis familiaris	ENSCAFG00000017311	4 retrocopies	retro_cfam_1278, retro_cfam_1678, retro_cfam_2089, retro_cfam_983,
Cavia porcellus	ENSCPOG00000007279	1 retrocopy	retro_cpor_150,
Dasypus novemcinctus	ENSDNOG00000019156	7 retrocopies	retro_dnov_1322, retro_dnov_1767, retro_dnov_329, retro_dnov_451, retro_dnov_848, retro_dnov_878, retro_dnov_944,
Equus caballus	ENSECAG00000010942	1 retrocopy	retro_ecab_390 ,
Felis catus	ENSFCAG00000012596	1 retrocopy	retro_fcat_1441,
Homo sapiens	ENSG00000143549	9 retrocopies	retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011, retro_hsap_2012, retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Myotis lucifugus	ENSMLUG00000013331	1 retrocopy	retro_mluc_1038,
Macaca mulatta	ENSMMUG00000010805	10 retrocopies	retro_mmul_1019, retro_mmul_1240, retro_mmul_1384, retro_mmul_1385, retro_mmul_1703, retro_mmul_1829, retro_mmul_2128, retro_mmul_2354, retro_mmul_314, retro_mmul_880,
Mustela putorius furo	ENSMPUG00000007875	1 retrocopy	retro_mputfur_604,
Mus musculus	ENSMUSG00000027940	1 retrocopy	retro_mmus_21,
Oryctolagus cuniculus	ENSOCUG00000011821	2 retrocopies	retro_ocun_699, retro_ocun_8,