RetrogeneDB ID: retro_btau_1638

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:17425702..17426167(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V0C
• Ensembl ID: ENSBTAG00000026428
• Aliases: ATP6V0C, PLP
• Description: V-type proton ATPase 16 kDa proteolipid subunit [Source:UniProtKB/Swiss-Prot;Acc:P23956]

Sequence

>retro_btau_1638
ATGTCCGAGGCCAAGAACGGCCCCGAGTAGGCTTCCTTTTTCGCGGTCATGGGTGCCTCAGCCGCCACGGTCTTCAGCGC
CCGGGGCGCCGCCTACGGTACAGCCAAGAGCGGCACGGGCATCGCAGCCATGTCTGTCATGCGGCCAGAGATGATCATGA
AGTCCATCATCCCGGTGGTCATGGCGGGGATCATCGCCATCTATGGTCTGGTGGTGGCAGTCCTCATCGCCAACTCCCTG
AATGACGGCATCAGTCTCTACAGGAGTTTCCTTCAGCTGGGCGCGGGCCTGAGCGTGGGCCTGAGCGGGCTGGCGGCGGG
CTTCGCCATCGGCATTGTCGGGGACGCAGGCGTGCGTGGCACCGCCCAGCAGCCGCGGCTCTTCGTGGGCATGATCCTCA
TCCTCATCTTCGCCGAGGTGCTCGGCCTCTACGGTCTCATCGTCGCCCTTATCCTCTCCACAAAG

Alignment

ORF - retro_btau_1638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSEAKNGPEYASFFAVMGASAAMVFSALGAAYGTAKSGTGIAAMSVMRPEMIMKSIIPVVMAGIIAIYGL
          MSEAKNGPE.ASFFAVMGASAA.VFSA.GAAYGTAKSGTGIAAMSVMRPEMIMKSIIPVVMAGIIAIYGL
Retrocopy MSEAKNGPE*ASFFAVMGASAATVFSARGAAYGTAKSGTGIAAMSVMRPEMIMKSIIPVVMAGIIAIYGL

Parental  VVAVLIANSLNDGISLYRSFLQLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEV
          VVAVLIANSLNDGISLYRSFLQLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEV
Retrocopy VVAVLIANSLNDGISLYRSFLQLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEV

Parental  LGLYGLIVALILSTK
          LGLYGLIVALILSTK
Retrocopy LGLYGLIVALILSTK

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	11.17 RPM
ERP005899_muscle	0.84 RPM	100.99 RPM
SRP017611_brain	0.23 RPM	163.90 RPM
SRP017611_kidney	0.12 RPM	83.34 RPM
SRP017611_liver	0.08 RPM	62.75 RPM
SRP030211_testis	2.76 RPM	70.47 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1638 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1638 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026428	1 retrocopy	retro_btau_1638 ,
Homo sapiens	ENSG00000185883	2 retrocopies	retro_hsap_1798, retro_hsap_3462,
Gorilla gorilla	ENSGGOG00000028600	2 retrocopies	retro_ggor_1323, retro_ggor_2335,
Macropus eugenii	ENSMEUG00000004597	2 retrocopies	retro_meug_1428, retro_meug_1837,
Myotis lucifugus	ENSMLUG00000026715	2 retrocopies	retro_mluc_2507, retro_mluc_294,
Monodelphis domestica	ENSMODG00000015439	5 retrocopies	retro_mdom_1669, retro_mdom_1739, retro_mdom_507, retro_mdom_84, retro_mdom_982,
Mus musculus	ENSMUSG00000024121	2 retrocopies	retro_mmus_2726, retro_mmus_2888,
Nomascus leucogenys	ENSNLEG00000009416	2 retrocopies	retro_nleu_1692, retro_nleu_2770,
Procavia capensis	ENSPCAG00000015060	1 retrocopy	retro_pcap_148,
Pan troglodytes	ENSPTRG00000007653	2 retrocopies	retro_ptro_1204, retro_ptro_2346,
Rattus norvegicus	ENSRNOG00000006542	1 retrocopy	retro_rnor_118,
Sarcophilus harrisii	ENSSHAG00000014251	1 retrocopy	retro_shar_194,
Ictidomys tridecemlineatus	ENSSTOG00000013420	3 retrocopies	retro_itri_119, retro_itri_387, retro_itri_691,
Drosophila melanogaster	FBgn0262736	3 retrocopies	retro_dmel_3, retro_dmel_38, retro_dmel_65,
Caenorhabditis elegans	R10E11.2	2 retrocopies	retro_cele_1, retro_cele_5,