RetrogeneDB ID: retro_btau_505

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:5323264..5323437(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM14A
• Ensembl ID: ENSBTAG00000005206
• Aliases: None
• Description: Transmembrane protein 14A [Source:UniProtKB/Swiss-Prot;Acc:P56982]

Sequence

>retro_btau_505
GGATCTTACTGTGTCTCCAATGAAAAGTGAGACGGTAAACTATCACTTTAACAGCTTTGTTCTTGGCCACTGTAATGGGC
GTGACATTTAAGGAGATCTGAGAAAATCACACCAGCTGTGCTGGTTGCTGGTTGAAGTCTCAGATGATCCTGAGACTTGT
TTCATTGCTGCTC

Alignment

ORF - retro_btau_505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.49 %
• Parental protein coverage: 58.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAYRVSNDKRDVKLSL-FTAFFLATIMGVRFK-RSKKIMPAGLVAGLSLL-MILRLVLLLL
          G.Y.VSN.K.D.KLSL..TA.FLAT.MGV.FK.RS.KI.PA.LVAG.SL..MILRLV.LLL
Retrocopy GSYCVSNEK*DGKLSL<LTALFLATVMGVTFK>RSEKITPAVLVAG*SLR<MILRLVSLLL

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	25.09 RPM
ERP005899_muscle	0.00 RPM	10.35 RPM
SRP017611_brain	0.05 RPM	26.13 RPM
SRP017611_kidney	0.00 RPM	13.10 RPM
SRP017611_liver	0.00 RPM	10.27 RPM
SRP030211_testis	0.01 RPM	18.40 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_505 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_505 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_505 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005206	1 retrocopy	retro_btau_505 ,
Bos taurus	ENSBTAG00000005808	1 retrocopy	retro_btau_970,
Latimeria chalumnae	ENSLACG00000012581	1 retrocopy	retro_lcha_64,
Microcebus murinus	ENSMICG00000016339	1 retrocopy	retro_mmur_211,
Mustela putorius furo	ENSMPUG00000008935	2 retrocopies	retro_mputfur_157, retro_mputfur_586,
Sorex araneus	ENSSARG00000005516	1 retrocopy	retro_sara_307,
Tupaia belangeri	ENSTBEG00000011162	1 retrocopy	retro_tbel_1562,
Tarsius syrichta	ENSTSYG00000004269	1 retrocopy	retro_tsyr_1783,
Tursiops truncatus	ENSTTRG00000015237	1 retrocopy	retro_ttru_1442,
Vicugna pacos	ENSVPAG00000004486	1 retrocopy	retro_vpac_450,