RetrogeneDB ID: retro_ecab_154

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:168583997..168584254(+)
• Located in intron of: ENSECAG00000023505

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPF
• Ensembl ID: ENSECAG00000019817
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide F [Source:HGNC Symbol;Acc:11162]

Sequence

>retro_ecab_154
ATGAGTTTGCCCCTCAATCCCAAACCTTTCCTCAATGGATTAACAGGAAAGCCAGTAATGGTGAAACTTAAGTGAGGAAT
GGAGTACAAAGACTACCTGGTATCTCTAGATAGCTATATGAACACGCAGCTTCCAAACACGAAGAATACATAGATGGAGC
ATTGTCTGGACATCTGGGTGAAGTTTTAATAAGGTGTGATAATGTCCTCTATATCAGGGGTGTTGAAGAAGAGGAAGAAG
ATGGGGAAATGAGAGAA

Alignment

ORF - retro_ecab_154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANT-EEYIDGALSGHLGEVLIRCNNV
          MSLPLNPKPFLNGLTGKPVMVKLK.GMEYK.YLVS.D.YMN.QL.NT.EEYIDGALSGHLGEVLIRC.NV
Retrocopy MSLPLNPKPFLNGLTGKPVMVKLK*GMEYKDYLVSLDSYMNTQLPNT<EEYIDGALSGHLGEVLIRCDNV

Parental  LYIRGVEEEEEDGEMRE
          LYIRGVEEEEEDGEMRE
Retrocopy LYIRGVEEEEEDGEMRE

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	8.21 RPM
SRP021940_cerebellum	0.00 RPM	10.75 RPM
SRP021940_embryo	0.00 RPM	17.03 RPM
SRP021940_placental_villous	0.00 RPM	8.32 RPM
SRP021940_synovial_membrane	0.03 RPM	8.51 RPM
SRP021940_testis	0.00 RPM	14.77 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_154 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_154 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_154 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239, retro_amel_42, retro_amel_883,
Bos taurus	ENSBTAG00000016271	1 retrocopy	retro_btau_765,
Equus caballus	ENSECAG00000019817	1 retrocopy	retro_ecab_154 ,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,
Homo sapiens	ENSG00000139343	3 retrocopies	retro_hsap_125, retro_hsap_2487, retro_hsap_2645,
Gorilla gorilla	ENSGGOG00000001127	2 retrocopies	retro_ggor_1549, retro_ggor_225,
Macaca mulatta	ENSMMUG00000009302	4 retrocopies	retro_mmul_1521, retro_mmul_361, retro_mmul_550, retro_mmul_893,
Mustela putorius furo	ENSMPUG00000007176	3 retrocopies	retro_mputfur_1309, retro_mputfur_377, retro_mputfur_941,
Mus musculus	ENSMUSG00000020018	4 retrocopies	retro_mmus_1060, retro_mmus_1197, retro_mmus_2537, retro_mmus_3210,
Nomascus leucogenys	ENSNLEG00000005835	3 retrocopies	retro_nleu_2259, retro_nleu_274, retro_nleu_651,
Pongo abelii	ENSPPYG00000004847	2 retrocopies	retro_pabe_381, retro_pabe_489,
Pteropus vampyrus	ENSPVAG00000009036	1 retrocopy	retro_pvam_1170,
Rattus norvegicus	ENSRNOG00000005556	4 retrocopies	retro_rnor_1822, retro_rnor_1849, retro_rnor_2926, retro_rnor_444,
Sus scrofa	ENSSSCG00000000895	1 retrocopy	retro_sscr_958,