RetrogeneDB ID: retro_ecab_943

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:97269425..97269800(+)
• Located in intron of: ENSECAG00000020512

Retrocopy information

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

Parental gene information

• Parental gene symbol: CIDEB
• Ensembl ID: ENSECAG00000010495
• Aliases: None
• Description: cell death-inducing DFFA-like effector b [Source:HGNC Symbol;Acc:1977]

Sequence

>retro_ecab_943
AAAGATGACACGTACCTGAGAGTGCCAAAGTTCAGGCAAAGCTGGGGCTCCAGCACGAGTGGGTGCTGTCACATGGCCTG
GGCTGGGAGAAGCCCAAGCACAGCAAGGACATTGCCCTTGTCACCCTCAACCTATCTAAGCAAAACCCGTGAGACCTCTT
TAGCAGCCTGAACGTCACAGCCACATTCTACGAGCTCTACTGCAGGAGTCATGACTTTCAAGGAGTTGGCCCAGAGAAAG
GACTCAGGGCACACCTCCAGTTGGACCTCCATGCTACTGTAAGGACTGGGCCACATGCTGCCAGGGATTTCCTCCCCCTT
CCACCACGCAATGGAGGCTCAGCAATGGTGGCGGCAGGGGTGCCTTCGTGCCTAC

Alignment

ORF - retro_ecab_943 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.15 %
• Parental protein coverage: 57.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDDTCLMVLESGQSWSPIRSR-VLSYGLGREKPKHSKDIARITFDVYKQNPRDLFGSLNIKATFYGLYSM
          .DDT.L.V....QSW....S..VLS.GLG.EKPKHSKDIA..T....KQNP.DLF.SLN..ATFY.LY..
Retrocopy KDDTYLRVPKFRQSWGSSTSG<VLSHGLGWEKPKHSKDIALVTLNLSKQNP*DLFSSLNVTATFYELYCR

Parental  SCDIQGLGPKKVLRELLR-WISALLQGLGHILLGISSTLRHVVEGAEQWQLQRQGRLHRY
          S.D.QG.GP.K.LR..L..W.S.LL.GLGH.L.GISS...H..E....W...RQG.L..Y
Retrocopy SHDFQGVGPEKGLRAHLQ>WTSMLL*GLGHMLPGISSPFHHAMEAQQWW---RQGCLRAY

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	0.18 RPM
SRP021940_cerebellum	0.05 RPM	0.52 RPM
SRP021940_embryo	0.00 RPM	9.13 RPM
SRP021940_placental_villous	0.00 RPM	0.24 RPM
SRP021940_synovial_membrane	0.00 RPM	0.36 RPM
SRP021940_testis	0.00 RPM	6.84 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_943 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_943 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_943 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016089	1 retrocopy	retro_amel_633,
Canis familiaris	ENSCAFG00000012240	1 retrocopy	retro_cfam_85,
Equus caballus	ENSECAG00000010495	1 retrocopy	retro_ecab_943 ,
Felis catus	ENSFCAG00000026821	1 retrocopy	retro_fcat_1418,
Pteropus vampyrus	ENSPVAG00000007036	1 retrocopy	retro_pvam_523,