RetrogeneDB ID: retro_ecab_587

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 22:19807802..19808094(+)
• Located in intron of: ENSECAG00000010855

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB2
• Ensembl ID: ENSECAG00000000877
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2, 8kDa [Source:HGNC Symbol;Acc:7697]

Sequence

>retro_ecab_587
GCGCCTTTCATTTGTGTTGGAGGCCACCTCTTCAGAGGGATCCGCTCGGGCAGCTGGAGGCAGTGGAGTCCGTCACACCA
GTGGTGGTGTGCATATCCAGCCCCGATACAGGCACTTCCCCCAGCTGACCAGATCCTAAGTGATCCAGGCAGAGTTGTTC
AGTGCAACCATGCGGTTCTGGATTCTCTGGTGCTTTTGGCATGACTCAGATGCTGGGCTGGATGACCTTCCACATCCAGA
TCCTTCCCAGTAGATGGATGAAGAACTAGGCCTCCTTCCTGATGATGAAGAC

Alignment

ORF - retro_ecab_587 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.41 %
• Parental protein coverage: 93.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APFVRLGGRLFLGRRV-RAAGGGARSAGGDVHIQPRYRQFPQLTRSQVIQAEFFSATMWFWILWRFWHDS
          APF...GG.LF.G.R...A.G.G.R...G.VHIQPRYR.FPQLTRS.VIQAE.FSATM.FWILW.FWHDS
Retrocopy APFICVGGHLFRGIRS>AAGGSGVRHTSGGVHIQPRYRHFPQLTRS*VIQAELFSATMRFWILWCFWHDS

Parental  DAVLGHFPYPDPSQWTDEELGILPDDED
          DA.L...P.PDPSQ..DEELG.LPDDED
Retrocopy DAGLDDLPHPDPSQ*MDEELGLLPDDED

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	12.81 RPM
SRP021940_cerebellum	0.00 RPM	44.04 RPM
SRP021940_embryo	0.03 RPM	28.79 RPM
SRP021940_placental_villous	0.00 RPM	26.08 RPM
SRP021940_synovial_membrane	0.00 RPM	11.34 RPM
SRP021940_testis	0.00 RPM	49.49 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_587 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_587 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_587 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011176	1 retrocopy	retro_acar_138,
Canis familiaris	ENSCAFG00000003930	3 retrocopies	retro_cfam_1673, retro_cfam_2184, retro_cfam_958,
Equus caballus	ENSECAG00000000877	1 retrocopy	retro_ecab_587 ,
Mustela putorius furo	ENSMPUG00000003423	3 retrocopies	retro_mputfur_132, retro_mputfur_1443, retro_mputfur_207,
Mus musculus	ENSMUSG00000002416	1 retrocopy	retro_mmus_1881,
Otolemur garnettii	ENSOGAG00000009644	1 retrocopy	retro_ogar_1405,
Ochotona princeps	ENSOPRG00000013184	2 retrocopies	retro_opri_1201, retro_opri_143,
Rattus norvegicus	ENSRNOG00000026616	2 retrocopies	retro_rnor_1153, retro_rnor_2449,
Sarcophilus harrisii	ENSSHAG00000015924	1 retrocopy	retro_shar_639,
Sus scrofa	ENSSSCG00000016495	1 retrocopy	retro_sscr_1149,
Ictidomys tridecemlineatus	ENSSTOG00000002566	1 retrocopy	retro_itri_1100,
Tursiops truncatus	ENSTTRG00000000547	2 retrocopies	retro_ttru_1567, retro_ttru_1910,