RetrogeneDB ID: retro_btau_1040

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 24:18478626..18478883(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMG4
• Ensembl ID: ENSBTAG00000031249
• Aliases: None
• Description: None

Sequence

>retro_btau_1040
TTCCTGCGGGTGGGGGCCATGCTGCACCGGCACAACCTCGCTGTGCCACGTGCACTGGCTATGATCCCGTCCGCATGCCT
ACTGCCCTCCTCAGAGACACAGCCCACAGGATGTCCACAGGCCTCACCCAGCACTTAGCCAGAAAAGCCAGCAAACAGGG
GTCTGTCAGCTATAGTCTTCCAAATACCAACAACAGCTTGGCATTACTGGTAGAAAACAGAATCAAGGGGGAAATGGCAG
CTTTTCCAGGGAAGTTC

Alignment

ORF - retro_btau_1040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.37 %
• Parental protein coverage: 69.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLWVGATPHLRNLAV-AMCTRYDSIPLSTALLGDTSDTMSTGLAQRLARKTSKQVFVSYNLPNTSSSFEL
          FL.VGA..H..NLAV.A.CT.YD.....TALL.DT...MSTGL.Q.LARK.SKQ..VSY.LPNT..S..L
Retrocopy FLRVGAMLHRHNLAV<ATCTGYDPVRMPTALLRDTAHRMSTGLTQHLARKASKQGSVSYSLPNTNNSLAL

Parental  LVESRIKEEMQAFPEKF
          LVE.RIK.EM.AFP.KF
Retrocopy LVENRIKGEMAAFPGKF

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	0.00 RPM	3.03 RPM
ERP005899_muscle	0.00 RPM	62.56 RPM
SRP017611_brain	0.00 RPM	9.27 RPM
SRP017611_kidney	0.00 RPM	14.40 RPM
SRP017611_liver	0.00 RPM	13.29 RPM
SRP030211_testis	0.00 RPM	19.17 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1040 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1040 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014430	1 retrocopy	retro_amel_1196,
Bos taurus	ENSBTAG00000031249	1 retrocopy	retro_btau_1040 ,
Myotis lucifugus	ENSMLUG00000024906	1 retrocopy	retro_mluc_802,
Rattus norvegicus	ENSRNOG00000039265	2 retrocopies	retro_rnor_1442, retro_rnor_766,
Sus scrofa	ENSSSCG00000001005	3 retrocopies	retro_sscr_362, retro_sscr_656, retro_sscr_657,
Tursiops truncatus	ENSTTRG00000006146	2 retrocopies	retro_ttru_1531, retro_ttru_1849,