RetrogeneDB ID: retro_ecab_725

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:69836628..69836787(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS28
• Ensembl ID: ENSECAG00000017256
• Aliases: None
• Description: ribosomal protein S28 [Source:HGNC Symbol;Acc:10418]

Sequence

>retro_ecab_725
ATAGACACGAGCTGTGTGCAGCTCATCAAGCTGGCCTGGGTCACCAAGGTGCTAGGCAGGACTGGCTCACAGGAACAGCA
CACACAGGCGCCCATGGAATTCATGGACAACACAAGCTTCTCCATCATCTGCAATGTGAAAGGCCCCATGAGCAAGGGC

Alignment

ORF - retro_ecab_725 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.7 %
• Parental protein coverage: 76.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREG
          .DTS.VQ.IKLA.VTKVLGRTGSQ.Q.TQ...EFMD.TS.SII.NVKGP...G
Retrocopy IDTSCVQLIKLAWVTKVLGRTGSQEQHTQAPMEFMDNTSFSIICNVKGPMSKG

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	473.24 RPM
SRP021940_cerebellum	0.00 RPM	276.28 RPM
SRP021940_embryo	0.00 RPM	496.88 RPM
SRP021940_placental_villous	0.00 RPM	281.93 RPM
SRP021940_synovial_membrane	0.00 RPM	465.23 RPM
SRP021940_testis	0.00 RPM	287.11 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_725 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_725 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_725 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004917	1 retrocopy	retro_amel_1359,
Bos taurus	ENSBTAG00000002468	1 retrocopy	retro_btau_1130,
Cavia porcellus	ENSCPOG00000022876	5 retrocopies	retro_cpor_1092, retro_cpor_1485, retro_cpor_1504, retro_cpor_176, retro_cpor_702,
Equus caballus	ENSECAG00000017256	1 retrocopy	retro_ecab_725 ,
Loxodonta africana	ENSLAFG00000029923	2 retrocopies	retro_lafr_168, retro_lafr_755,
Myotis lucifugus	ENSMLUG00000023621	1 retrocopy	retro_mluc_2040,
Macaca mulatta	ENSMMUG00000028895	3 retrocopies	retro_mmul_122, retro_mmul_182, retro_mmul_807,
Monodelphis domestica	ENSMODG00000003890	1 retrocopy	retro_mdom_291,
Mus musculus	ENSMUSG00000067288	3 retrocopies	retro_mmus_2949, retro_mmus_3283, retro_mmus_91,
Rattus norvegicus	ENSRNOG00000042886	2 retrocopies	retro_rnor_95, retro_rnor_96,