RetrogeneDB ID: retro_btau_1528

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:35557617..35557961(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000017481
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPL53
• Ensembl ID: ENSBTAG00000016599
• Aliases: None
• Description: 39S ribosomal protein L53, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q2HJF1]

Sequence

>retro_btau_1528
ATGGCGGCGGCCTTGGCTCGGCTCGGACTCTGCTCGGTCAAGCAGGTTCGGGTTCAGTTCTGTTCCTTCAAGAAGAACTT
GGAATCGACGAAGACCTTCCACCAGGCAGTGAGCAGCGAGAAAGTTCGCTGTACGAACCTCAACTGCTCAGTGATTGTAG
AAATGAGGCACAAGGGCTCCGAGCCTTGCGTGGACGTGCTGTTCGGAGACGGGCATTGTTGATTATGCGCAGCGCGCACC
TCACCGCCCACACCGCCCAGGAAATGCTCACGGCCTTCGCCTCCCACATCCAGGCCAAGGGCACGGCAGGAAGCAGGGAC
AAGCCAAGCGCCAGTACCAGGCGC

Alignment

ORF - retro_btau_1528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAALARLGLRSVKQVRVQFCPFEKNVESTRTFLQAVSSEKVRSTNLNCSVIADVRHDGSEPCVDVLFGD
          MAAALARLGL.SVKQVRVQFC.F.KN.EST.TF.QAVSSEKVR.TNLNCSVI...RH.GSEPCVDVLFGD
Retrocopy MAAALARLGLCSVKQVRVQFCSFKKNLESTKTFHQAVSSEKVRCTNLNCSVIVEMRHKGSEPCVDVLFGD

Parental  GH-RLIMRGAHLTA---QEMLSAFASHIQARGAAASGDKPSASTGR
          GH..LIMR.AHLTA...QEML.AFASHIQA.G.A.S.DKPSAST.R
Retrocopy GH<LLIMRSAHLTAHTAQEMLTAFASHIQAKGTAGSRDKPSASTRR

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	0.07 RPM	30.21 RPM
ERP005899_muscle	0.05 RPM	38.80 RPM
SRP017611_brain	0.00 RPM	23.84 RPM
SRP017611_kidney	0.00 RPM	37.64 RPM
SRP017611_liver	0.08 RPM	29.30 RPM
SRP030211_testis	0.40 RPM	38.75 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1528 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1528 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016599	3 retrocopies	retro_btau_1132, retro_btau_1528 , retro_btau_799,
Nomascus leucogenys	ENSNLEG00000000672	1 retrocopy	retro_nleu_44,
Oryctolagus cuniculus	ENSOCUG00000015342	1 retrocopy	retro_ocun_372,
Pan troglodytes	ENSPTRG00000033835	1 retrocopy	retro_ptro_90,
Tarsius syrichta	ENSTSYG00000002278	2 retrocopies	retro_tsyr_1300, retro_tsyr_1840,