RetrogeneDB ID: retro_ecab_838

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:58704174..58704383(+)
• Located in intron of: ENSECAG00000011835

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFS6
• Ensembl ID: ENSECAG00000021690
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 6, 13kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7713]

Sequence

>retro_ecab_838
CGGCTGCTGGGCTGGAGCAGAGGGGCGGCGCCGAGCCCACCCGGGGTGCCAGGCACTTCAGGGTGTGGACCTCACCGACT
GGGGAGAAGGTCACGCACGCTGGCCAGGTTTATGATGATGGAGACGACAAGAGGATTCGGTTTGTAGGGCATCAGAAAGA
GGTGAATGAAAACTTCGCCACTGATTTGATAGCAGAGCAACCCATGAGT

Alignment

ORF - retro_ecab_838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.24 %
• Parental protein coverage: 56.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLLGRGGGAALSLPG-GARCFGVRTSPTGEKVTHTGQAYGAEDYRRIRFVGRQKEVNENFAIDLIAEQPV
          RLLG...GAA.S.PG.GAR.F.V.TSPTGEKVTH.GQ.Y...D..RIRFVG.QKEVNENFA.DLIAEQP.
Retrocopy RLLGWSRGAAPSPPG<GARHFRVWTSPTGEKVTHAGQVYDDGDDKRIRFVGHQKEVNENFATDLIAEQPM

Parental  S
          S
Retrocopy S

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	0.30 RPM	20.96 RPM
SRP021940_cerebellum	0.42 RPM	46.01 RPM
SRP021940_embryo	0.59 RPM	35.75 RPM
SRP021940_placental_villous	0.24 RPM	28.19 RPM
SRP021940_synovial_membrane	0.49 RPM	21.28 RPM
SRP021940_testis	0.19 RPM	44.76 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_838 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_838 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_838 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010930	2 retrocopies	retro_amel_213, retro_amel_228,
Bos taurus	ENSBTAG00000009914	2 retrocopies	retro_btau_302, retro_btau_333,
Callithrix jacchus	ENSCJAG00000019382	1 retrocopy	retro_cjac_1552,
Equus caballus	ENSECAG00000021690	3 retrocopies	retro_ecab_701, retro_ecab_838 , retro_ecab_917,
Homo sapiens	ENSG00000145494	1 retrocopy	retro_hsap_2838,
Latimeria chalumnae	ENSLACG00000004625	1 retrocopy	retro_lcha_95,
Loxodonta africana	ENSLAFG00000005708	1 retrocopy	retro_lafr_5,
Myotis lucifugus	ENSMLUG00000016888	1 retrocopy	retro_mluc_1750,
Macaca mulatta	ENSMMUG00000004447	1 retrocopy	retro_mmul_1473,
Monodelphis domestica	ENSMODG00000001425	1 retrocopy	retro_mdom_207,
Mus musculus	ENSMUSG00000021606	1 retrocopy	retro_mmus_3044,
Nomascus leucogenys	ENSNLEG00000011199	1 retrocopy	retro_nleu_1593,
Oryctolagus cuniculus	ENSOCUG00000004581	2 retrocopies	retro_ocun_1011, retro_ocun_1624,
Pongo abelii	ENSPPYG00000015323	1 retrocopy	retro_pabe_2350,
Pan troglodytes	ENSPTRG00000016706	1 retrocopy	retro_ptro_1924,
Rattus norvegicus	ENSRNOG00000023387	1 retrocopy	retro_rnor_1619,
Rattus norvegicus	ENSRNOG00000049394	1 retrocopy	retro_rnor_1618,
Sarcophilus harrisii	ENSSHAG00000017779	1 retrocopy	retro_shar_176,
Ictidomys tridecemlineatus	ENSSTOG00000003715	1 retrocopy	retro_itri_496,