RetrogeneDB ID: retro_btau_1203

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:1684837..1685099(+)
• Located in intron of: ENSBTAG00000008652

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGC3248
• Ensembl ID: ENSBTAG00000006410
• Aliases: None
• Description: dynactin subunit 5 [Source:RefSeq peptide;Acc:NP_001019655]

Sequence

>retro_btau_1203
TCAGCAAAGGTTGCATTTTTTCCTTTACATATTGGGGACCACATCTTTACTGAGGAAGATCGTGTGGTCAACGCAGCTCA
TATTGGCTCTTATGTTCACATTGGCAAGAACTGTGTGACTGAGTGCTGATGTGTCTTGAAAGGCTGTTGAAAAATTCTTG
ACAACACAGTATTACCCCCAGAAACTGTGGTCCCACCATTCACCGTCTTCTCAGGCTGCCCAGGACTTTTCTCAGGGGAG
CTTCCAGAATGTACTCAGGAGC

Alignment

ORF - retro_btau_1203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.68 %
• Parental protein coverage: 53.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRCVLKDCCKILDNTVLPPETVVPPFTIF
          S..VAFFPLHIGDH.F.EED.VVNAA.IGSYVH.GKNCV....CVLK.C.KILDNTVLPPETVVPPFT.F
Retrocopy SAKVAFFPLHIGDHIFTEEDRVVNAAHIGSYVHIGKNCVTEC*CVLKGC*KILDNTVLPPETVVPPFTVF

Parental  SGCPGLFS-GSSQNVPRS
          SGCPGLFS.GS.QNV.RS
Retrocopy SGCPGLFS>GSFQNVLRS

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	16.73 RPM
ERP005899_muscle	0.00 RPM	32.36 RPM
SRP017611_brain	0.00 RPM	27.96 RPM
SRP017611_kidney	0.00 RPM	29.16 RPM
SRP017611_liver	0.00 RPM	15.55 RPM
SRP030211_testis	0.04 RPM	25.96 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1203 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1203 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1203 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006410	1 retrocopy	retro_btau_1203 ,
Callithrix jacchus	ENSCJAG00000020623	1 retrocopy	retro_cjac_1687,
Homo sapiens	ENSG00000166847	1 retrocopy	retro_hsap_260,
Gorilla gorilla	ENSGGOG00000012834	1 retrocopy	retro_ggor_309,
Microcebus murinus	ENSMICG00000007806	1 retrocopy	retro_mmur_1082,
Myotis lucifugus	ENSMLUG00000012148	1 retrocopy	retro_mluc_140,
Mus musculus	ENSMUSG00000030868	2 retrocopies	retro_mmus_2733, retro_mmus_625,
Nomascus leucogenys	ENSNLEG00000012015	1 retrocopy	retro_nleu_863,
Pongo abelii	ENSPPYG00000007194	2 retrocopies	retro_pabe_1729, retro_pabe_405,
Pan troglodytes	ENSPTRG00000007891	1 retrocopy	retro_ptro_220,
Rattus norvegicus	ENSRNOG00000018048	2 retrocopies	retro_rnor_1351, retro_rnor_1847,