RetrogeneDB ID: retro_ecab_859

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:49662928..49663160(-)
• Located in intron of: ENSECAG00000015266

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D3
• Ensembl ID: ENSECAG00000020678
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 3 [Source:HGNC Symbol;Acc:12476]

Sequence

>retro_ecab_859
TCTACAGGTCCAGCTGGGGATGATGAGTTTCACTGGCGAGCCACAATTATGGAACCCAATGACAGCACATATCAAGGCAA
TGTATTTTTTTAACAATTCATTCTCCTACAGACTACCCCTTCAAATCACCTAAGGTTGCATTTACAAGAATTTATTATCA
AATATTAACAATAATGGCAGCATTTGTCTTGATATTCTAAGATCACAGTGGTCTCTTGCTTTAACTATTTCT

Alignment

ORF - retro_ecab_859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.25 %
• Parental protein coverage: 56.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SAGPVGDDMFHWQATIMGPNDSPYQGGVFF-LTIHFPTDYPFKPPKVAFTTRIYHP-NINSNGSICLDIL
          S.GP.GDD.FHW.ATIM.PNDS.YQG.VFF.LTIH.PTDYPFK.PKVAFT.RIY...NIN.NGSICLDIL
Retrocopy STGPAGDDEFHWRATIMEPNDSTYQGNVFF<LTIHSPTDYPFKSPKVAFT-RIYYQ<NINNNGSICLDIL

Parental  RSQWSPALTIS
          RSQWS.ALTIS
Retrocopy RSQWSLALTIS

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	36.36 RPM
SRP021940_cerebellum	0.00 RPM	36.77 RPM
SRP021940_embryo	0.03 RPM	43.78 RPM
SRP021940_placental_villous	0.00 RPM	73.90 RPM
SRP021940_synovial_membrane	0.03 RPM	34.67 RPM
SRP021940_testis	0.00 RPM	88.18 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_859 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_859 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_859 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1261

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004649	2 retrocopies	retro_chof_2549, retro_chof_439,
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
Callithrix jacchus	ENSCJAG00000015492	3 retrocopies	retro_cjac_512, retro_cjac_657, retro_cjac_791,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
Dipodomys ordii	ENSDORG00000006762	2 retrocopies	retro_dord_172, retro_dord_323,
Equus caballus	ENSECAG00000007233	1 retrocopy	retro_ecab_196,
Equus caballus	ENSECAG00000019274	1 retrocopy	retro_ecab_116,
Equus caballus	ENSECAG00000020678	1 retrocopy	retro_ecab_859 ,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Gorilla gorilla	ENSGGOG00000010832	1 retrocopy	retro_ggor_953,
Macropus eugenii	ENSMEUG00000004256	6 retrocopies	retro_meug_1034, retro_meug_1503, retro_meug_2138, retro_meug_564, retro_meug_787, retro_meug_89,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Sus scrofa	ENSSSCG00000024306	1 retrocopy	retro_sscr_783,
Sus scrofa	ENSSSCG00000029822	4 retrocopies	retro_sscr_1016, retro_sscr_672, retro_sscr_673, retro_sscr_918,
Ictidomys tridecemlineatus	ENSSTOG00000013481	6 retrocopies	retro_itri_1222, retro_itri_1474, retro_itri_1628, retro_itri_463, retro_itri_672, retro_itri_998,
Tupaia belangeri	ENSTBEG00000000270	5 retrocopies	retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,