RetrogeneDB ID: retro_ecab_704

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 29:25133517..25133846(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCL7C
• Ensembl ID: ENSECAG00000000482
• Aliases: None
• Description: B-cell CLL/lymphoma 7C [Source:HGNC Symbol;Acc:1006]

Sequence

>retro_ecab_704
TTGCAAAAGGGCACTGAGCTCGGTGCTGGGGGCCTGCCCCTAGCCAGCTACCCTGTGTCACCTGCCAAACCACTGGAAGG
GGTCCCAGAGGATGCTCAGCCTCCATGGCTGGGCCAAGAGAGAGATCTCAGGGGCATAATAACAGGTGGCACTGATAAAC
CCCCAAAGTGACCCAGGAGGAGTCTGTTCCAGAACTGCTGGAGGATGAGGCCACTGAAGCTTAGCCCATCCTTGAGCCAC
TGCTATATGTGCCTGAGGCAGCCCAGGGTGACACAGAGGACTCGGAGGACATCCCTCCACTCAAGCGCGTCTGCCCAGAT
ATCCCCAAC

Alignment

ORF - retro_ecab_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.37 %
• Parental protein coverage: 53.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQKGTEPSPGGTPQPSRPVSPAGPPEGVPEDAQPPRLGQERDPGGITAGGTDEPPM-LTKEEPVPELLEA
          LQKGTE...GG.P..S.PVSPA.P.EGVPEDAQPP.LGQERD..GI..GGTD.PP...T.EE.VPELLE.
Retrocopy LQKGTELGAGGLPLASYPVSPAKPLEGVPEDAQPPWLGQERDLRGIITGGTDKPPK<VTQEESVPELLED

Parental  EAPEAYPVFEPVPPVPEAAQGDTEDSEGAPPLKRICPNAPD
          EA.EA.P..EP...VPEAAQGDTEDSE..PPLKR.CP..P.
Retrocopy EATEA*PILEPLLYVPEAAQGDTEDSEDIPPLKRVCPDIPN

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	25.86 RPM
SRP021940_cerebellum	0.00 RPM	13.35 RPM
SRP021940_embryo	0.00 RPM	39.89 RPM
SRP021940_placental_villous	0.00 RPM	25.21 RPM
SRP021940_synovial_membrane	0.00 RPM	35.14 RPM
SRP021940_testis	0.00 RPM	16.11 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_704 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_704 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_704 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007604	2 retrocopies	retro_amel_1090, retro_amel_1613,
Bos taurus	ENSBTAG00000008412	1 retrocopy	retro_btau_618,
Canis familiaris	ENSCAFG00000016715	1 retrocopy	retro_cfam_898,
Dipodomys ordii	ENSDORG00000001676	1 retrocopy	retro_dord_517,
Equus caballus	ENSECAG00000000482	1 retrocopy	retro_ecab_704 ,
Felis catus	ENSFCAG00000029090	1 retrocopy	retro_fcat_1969,
Macaca mulatta	ENSMMUG00000003225	13 retrocopies	retro_mmul_1247, retro_mmul_1613, retro_mmul_1818, retro_mmul_2108, retro_mmul_2153, retro_mmul_2644, retro_mmul_390, retro_mmul_724, retro_mmul_740, retro_mmul_750, retro_mmul_755, retro_mmul_791, retro_mmul_975,
Mustela putorius furo	ENSMPUG00000011988	1 retrocopy	retro_mputfur_954,