RetrogeneDB ID: retro_btau_1329

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:93662298..93662629(+)
• Located in intron of: ENSBTAG00000003449

Retrocopy information

• Ensembl ID: ENSBTAG00000047361
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NME2
• Ensembl ID: ENSBTAG00000047186
• Aliases: None
• Description: Nucleoside diphosphate kinase B [Source:UniProtKB/Swiss-Prot;Acc:Q3T0Q4]

Sequence

>retro_btau_1329
GAGCGCACCTTTATTGCTATCAAGCCGGACGGCGTGCAGCGCGGCCTGTGTGGGCGAGATCATCAAGCGCTTCGAGCAGA
AGGGATTCCTCCTTGTGGCCATGAAGTTCCTTCAGGCCTCTGAGGAACTCCTGAAGCAGCACTACATTGACCTGAAAGAC
CGCCCATTCTTTCCCGGCCTGGTGAAGTACATGAACTCAGGGCCAGTTGTGGCCATGGTCTGGGAGGGCCTGAATGTAGT
GAAGACAGGACGAGTGATGCTTGGGGAGACCAACCCAGCAGATTCTAAGCCGGGCACCATTCGTGGTGACTTCTGCATTC
AAGTTGGCAGG

Alignment

ORF - retro_btau_1329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.2 %
• Parental protein coverage: 96.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERTFIAIKPDGVQRGL-VGEIIKRFEQKGFRLVAMKFLQASEELLKQHYIDLKDRPFFPGLVKYMNSGPV
          ERTFIAIKPDGVQRGL.VGEIIKRFEQKGF.LVAMKFLQASEELLKQHYIDLKDRPFFPGLVKYMNSGPV
Retrocopy ERTFIAIKPDGVQRGL>VGEIIKRFEQKGFLLVAMKFLQASEELLKQHYIDLKDRPFFPGLVKYMNSGPV

Parental  VAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGR
          VAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGR
Retrocopy VAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGR

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	8.58 RPM	3.82 RPM
ERP005899_muscle	30.93 RPM	61.55 RPM
SRP017611_brain	16.22 RPM	16.31 RPM
SRP017611_kidney	31.41 RPM	28.45 RPM
SRP017611_liver	12.08 RPM	10.50 RPM
SRP030211_testis	6.27 RPM	7.78 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1329 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1329 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1329 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Bos taurus	ENSBTAG00000004651	1 retrocopy	retro_btau_1707,
Bos taurus	ENSBTAG00000047186	1 retrocopy	retro_btau_1329 ,
Equus caballus	ENSECAG00000021658	1 retrocopy	retro_ecab_404,
Felis catus	ENSFCAG00000006742	5 retrocopies	retro_fcat_1083, retro_fcat_1117, retro_fcat_1475, retro_fcat_216, retro_fcat_663,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Loxodonta africana	ENSLAFG00000007784	1 retrocopy	retro_lafr_636,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Macaca mulatta	ENSMMUG00000001940	1 retrocopy	retro_mmul_1827,
Mustela putorius furo	ENSMPUG00000015573	4 retrocopies	retro_mputfur_1236, retro_mputfur_1590, retro_mputfur_327, retro_mputfur_912,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Sus scrofa	ENSSSCG00000017591	1 retrocopy	retro_sscr_854,
Tupaia belangeri	ENSTBEG00000013053	6 retrocopies	retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,
Tursiops truncatus	ENSTTRG00000007433	1 retrocopy	retro_ttru_1821,