RetrogeneDB ID: retro_btau_360

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:100092611..100092891(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC61B
• Ensembl ID: ENSBTAG00000002457
• Aliases: None
• Description: protein transport protein Sec61 subunit beta [Source:RefSeq peptide;Acc:NP_001068760]

Sequence

>retro_btau_360
ATGCCTGGCCCGGCCCCAGTGCCACTAACGTGGGTCCTCATGGCGCTCTCCCAGCAAAGCAGTGGCGGCCCGGGCGGCGG
GATCCACCGTCCAACAGAGGAAGAATGCCAGCTGTGGAACAAGGAGCACAGGCCATACGACCTCAGTGGGCACTGGAGGG
ATGGGGCGATTCTATACAGAGGATTTACCAGAGCTCAAAGTGGGCCCAGCTCCAGTATTGGTTATGAGTCTTTTGTTCAT
TGCTTCTATATTTATGTTGCACATTTGGTGCAAGTACACT

Alignment

ORF - retro_btau_360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.42 %
• Parental protein coverage: 97.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPGPAP-SGTNVG-SSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDSPGLKV
          MPGPAP.S.TNVG.SS.RSPSKAVAARAAGSTV.QRKNASCGTRS.G.TTS.GTGGM.RFYTED.P.LKV
Retrocopy MPGPAP<SATNVG<SSWRSPSKAVAARAAGSTVQQRKNASCGTRSTGHTTSVGTGGMGRFYTEDLPELKV

Parental  GPVPVLVMSLLFIASVFMLHIWGKYT
          GP.PVLVMSLLFIAS.FMLHIW.KYT
Retrocopy GPAPVLVMSLLFIASIFMLHIWCKYT

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	44.05 RPM
ERP005899_muscle	0.00 RPM	79.50 RPM
SRP017611_brain	0.00 RPM	11.19 RPM
SRP017611_kidney	0.00 RPM	43.98 RPM
SRP017611_liver	0.00 RPM	126.55 RPM
SRP030211_testis	0.00 RPM	24.64 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_360 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_360 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002457	3 retrocopies	retro_btau_1053, retro_btau_360 , retro_btau_791,
Callithrix jacchus	ENSCJAG00000011279	1 retrocopy	retro_cjac_503,
Equus caballus	ENSECAG00000026930	1 retrocopy	retro_ecab_711,
Echinops telfairi	ENSETEG00000005293	4 retrocopies	retro_etel_1777, retro_etel_1889, retro_etel_483, retro_etel_695,
Homo sapiens	ENSG00000106803	1 retrocopy	retro_hsap_871,
Gorilla gorilla	ENSGGOG00000004205	1 retrocopy	retro_ggor_708,
Macropus eugenii	ENSMEUG00000000321	1 retrocopy	retro_meug_1921,
Microcebus murinus	ENSMICG00000011121	4 retrocopies	retro_mmur_1037, retro_mmur_1631, retro_mmur_435, retro_mmur_543,
Myotis lucifugus	ENSMLUG00000001097	1 retrocopy	retro_mluc_2170,
Macaca mulatta	ENSMMUG00000010661	1 retrocopy	retro_mmul_86,
Mus musculus	ENSMUSG00000053317	2 retrocopies	retro_mmus_1377, retro_mmus_2679,
Nomascus leucogenys	ENSNLEG00000017055	1 retrocopy	retro_nleu_2844,
Otolemur garnettii	ENSOGAG00000004168	3 retrocopies	retro_ogar_1132, retro_ogar_2671, retro_ogar_823,
Pongo abelii	ENSPPYG00000019441	1 retrocopy	retro_pabe_680,
Pan troglodytes	ENSPTRG00000021184	1 retrocopy	retro_ptro_606,
Rattus norvegicus	ENSRNOG00000006345	1 retrocopy	retro_rnor_1589,