RetrogeneDB ID: retro_btau_1130

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 27:15623111..15623317(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000006046
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS28
• Ensembl ID: ENSBTAG00000002468
• Aliases: None
• Description: 40S ribosomal protein S28 [Source:UniProtKB/Swiss-Prot;Acc:Q56JX6]

Sequence

>retro_btau_1130
ATGGACACGAGCCGTGTGCAGCCCATCAAGCTTGCCAGGGTCACCAAGGTGTTGGCAGGACCGGTTCTCAGGGACAGTGC
ACGCAGGTGCGCGTAGAATTCATGGACGACACGAGCCGCTCCATCATCCGAAACGTGAAAGGCCCCGAGCGCGAGGGCGA
CGTGCTCACCCTGTTGGAGTCAGAGCGAGAGGCTCGGAGGCTGCGC

Alignment

ORF - retro_btau_1130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.14 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDTSRVQPIKLARVTKVL-GRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR
          MDTSRVQPIKLARVTKVL.GRTGSQGQCTQVRVEFMDDTSRSIIRNVKGP.REGDVLTLLESEREARRLR
Retrocopy MDTSRVQPIKLARVTKVL<GRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPEREGDVLTLLESEREARRLR

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
ERP005899_liver	0.14 RPM	30.06 RPM
ERP005899_muscle	2.69 RPM	795.37 RPM
SRP017611_brain	0.32 RPM	75.05 RPM
SRP017611_kidney	0.30 RPM	151.68 RPM
SRP017611_liver	0.53 RPM	107.30 RPM
SRP030211_testis	1.02 RPM	67.22 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1130 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1130 has 0 orthologous retrocopies within eutheria group .

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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,