RetrogeneDB ID: retro_ecab_711

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:32072072..32072329(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC61B
• Ensembl ID: ENSECAG00000026930
• Aliases: None
• Description: Sec61 beta subunit [Source:HGNC Symbol;Acc:16993]

Sequence

>retro_ecab_711
GTGGGCCGGGCCCTGGTGGACCCGCACAGGCTCCTCGGAGCCCTCCCAGTGGGGTCCCGGGCTGCCCCGGGCAGAGGAAG
AAGCCGGCGTGGGACGGGGAGCGCAGGCCGCACGACCTTGGCAGGCTCTGGGGGGCCGGGGCGATCCTGCACAGAGGGTC
ACCGGGCCTCAGCGTCGGCCCTGTGCCATTACTGGTTGTGAGTCTTCTGATCGCTGCTTCTGTATTTATGTCGCACATTT
GGAGCAAGGACATTCGG

Alignment

ORF - retro_ecab_711 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.87 %
• Parental protein coverage: 88.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VGSSGRSPSKAVAARAAGSTVRQRKNASC-GTRSAGRTTSAGTGGMWRFYTED-SPGLKVGPVPVLVMSL
          VG.....P.....A...GS........S..GT.SAGRTT.AG.GG..R..TE..SPGL.VGPVP.LV.SL
Retrocopy VGRALVDPHRLLGALPVGSRAAPGRGRSRRGTGSAGRTTLAGSGGPGRSCTEG<SPGLSVGPVPLLVVSL

Parental  LFIASVFMLHIWGKYTR
          L..ASVFM.HIW.K..R
Retrocopy LIAASVFMSHIWSKDIR

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	0.24 RPM	29.57 RPM
SRP021940_cerebellum	0.21 RPM	17.76 RPM
SRP021940_embryo	0.03 RPM	31.94 RPM
SRP021940_placental_villous	0.05 RPM	30.60 RPM
SRP021940_synovial_membrane	0.08 RPM	33.22 RPM
SRP021940_testis	0.06 RPM	62.86 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_711 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_711 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_711 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002457	3 retrocopies	retro_btau_1053, retro_btau_360, retro_btau_791,
Equus caballus	ENSECAG00000026930	1 retrocopy	retro_ecab_711 ,
Echinops telfairi	ENSETEG00000005293	4 retrocopies	retro_etel_1777, retro_etel_1889, retro_etel_483, retro_etel_695,
Gorilla gorilla	ENSGGOG00000004205	1 retrocopy	retro_ggor_708,
Macropus eugenii	ENSMEUG00000000321	1 retrocopy	retro_meug_1921,
Microcebus murinus	ENSMICG00000011121	4 retrocopies	retro_mmur_1037, retro_mmur_1631, retro_mmur_435, retro_mmur_543,
Myotis lucifugus	ENSMLUG00000001097	1 retrocopy	retro_mluc_2170,
Macaca mulatta	ENSMMUG00000010661	1 retrocopy	retro_mmul_86,
Mus musculus	ENSMUSG00000053317	2 retrocopies	retro_mmus_1377, retro_mmus_2679,
Nomascus leucogenys	ENSNLEG00000017055	1 retrocopy	retro_nleu_2844,
Otolemur garnettii	ENSOGAG00000004168	3 retrocopies	retro_ogar_1132, retro_ogar_2671, retro_ogar_823,
Pongo abelii	ENSPPYG00000019441	1 retrocopy	retro_pabe_680,