RetrogeneDB ID: retro_btau_1707

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:67929103..67929429(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000046230
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NME1
• Ensembl ID: ENSBTAG00000004651
• Aliases: NME1, NBR-A, NBR-B, NME1-1
• Description: nucleoside diphosphate kinase A 1 [Source:RefSeq peptide;Acc:NP_991387]

Sequence

>retro_btau_1707
TCTGATGAACACTTTGAGCAGCAATATGTTGCTCTGAAAGACCGCTCATTCTTCCCAGGGCTAGAGAAGTGCATGGACTC
AAGATCAGTTGTGGCCATGGTCTGGAAGGGCCTGGATATGGTTAAGTCAGGGAAGGCTGATGTTTGGGGAGACAACCTGG
CAGACTCTAAGTTGGGCACCATTCTCAGGACCTCTGCACTCAAGTTGGCAGGAACATCATTTGTGGTAGTAATTCAGTAG
AAAGTCCTGAAAAAGAAACCAGCCTACGGTTTAAGCTGGAAGAATTGGTTGATGACATGTCTTGTGCTTATGACTGGATC
CATGAA

Alignment

ORF - retro_btau_1707 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.93 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SEDLLKEHYIDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKT-GRVMLGET-NPADSKPGTI-RGDFCI
          S.......Y..LKDR.FF.GL.K.M.S..VVAMVW.GL..VK..GR.M.GET.N.ADSK.GTI...D.C.
Retrocopy SDEHFEQQYVALKDRSFFPGLEKCMDSRSVVAMVWKGLDMVKS>GRLMFGET<NLADSKLGTI<SQDLCT

Parental  QVGRNIIHGSDSVESAEKEIALWFHPEELVNYKNCAQNWIYE
          QVGRNII.GS.SVES.EKE..L.F..EELV....CA..WI.E
Retrocopy QVGRNIICGSNSVESPEKETSLRFKLEELVDDMSCAYDWIHE

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	11.25 RPM
ERP005899_muscle	0.00 RPM	36.05 RPM
SRP017611_brain	0.00 RPM	8.72 RPM
SRP017611_kidney	0.00 RPM	15.06 RPM
SRP017611_liver	0.00 RPM	24.01 RPM
SRP030211_testis	0.00 RPM	13.86 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1707 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1707 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1707 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004651	1 retrocopy	retro_btau_1707 ,
Bos taurus	ENSBTAG00000047186	1 retrocopy	retro_btau_1329,
Canis familiaris	ENSCAFG00000023628	7 retrocopies	retro_cfam_117, retro_cfam_1645, retro_cfam_37, retro_cfam_676, retro_cfam_69, retro_cfam_832, retro_cfam_96,
Gorilla gorilla	ENSGGOG00000016526	1 retrocopy	retro_ggor_71,
Monodelphis domestica	ENSMODG00000028492	1 retrocopy	retro_mdom_503,
Mustela putorius furo	ENSMPUG00000015559	5 retrocopies	retro_mputfur_1093, retro_mputfur_1357, retro_mputfur_442, retro_mputfur_667, retro_mputfur_997,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581,
Nomascus leucogenys	ENSNLEG00000007919	2 retrocopies	retro_nleu_1029, retro_nleu_1030,
Oryctolagus cuniculus	ENSOCUG00000022135	1 retrocopy	retro_ocun_1728,
Pan troglodytes	ENSPTRG00000009415	1 retrocopy	retro_ptro_91,
Rattus norvegicus	ENSRNOG00000002693	3 retrocopies	retro_rnor_1198, retro_rnor_1600, retro_rnor_704,