RetrogeneDB ID: retro_btau_1106

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 26:40282889..40283168(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VMA21
• Ensembl ID: ENSBTAG00000006296
• Aliases: None
• Description: Vacuolar ATPase assembly integral membrane protein VMA21 [Source:UniProtKB/Swiss-Prot;Acc:A2VDK9]

Sequence

>retro_btau_1106
GCCGCCGGCAACGCTGCCGAGCCCAAGCCCGAAGGCGGCAGCCTGGCGACCACTTTCAAGATTTTTCTCCTTTTTGCAGG
ACTGATGGTTAAAGTTCCTGTGGGGTTGTATTTTTCCTGCAAATTGCTGCTTTTCCAAAGCCTCCTGTTAATGTCCCCCG
ATGACAGTGGCTTTTACGCAACCATTGTCGCGGTGGTGGGGCTGCATGTGGTGCTGGCGGTGTTTGTGTTCATCGTGTGG
AAGGAGGGCATGCCTGACTGGCGGGAAGAGAAAAACGAG

Alignment

ORF - retro_btau_1106 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.53 %
• Parental protein coverage: 94.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AALNALQPSDFRNESSLASTLKTLLFFTALMITVPIGLYFTTKSYVFEGAFGMSNRDSYFYAAIVAVVAV
          AA.NA..P.......SLA.T.K..L.F..LM..VP.GLYF..K...F.....MS..DS.FYA.IVAVV..
Retrocopy AAGNAAEPKP--EGGSLATTFKIFLLFAGLMVKVPVGLYFSCKLLLFQSLLLMSPDDSGFYATIVAVVGL

Parental  HVVLALFVYVAWNEGSRQWREGKQD
          HVVLA.FV...W.EG...WRE.K..
Retrocopy HVVLAVFVFIVWKEGMPDWREEKNE

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	42.90 RPM
ERP005899_muscle	0.11 RPM	39.91 RPM
SRP017611_brain	36.68 RPM	61.58 RPM
SRP017611_kidney	0.24 RPM	107.40 RPM
SRP017611_liver	0.08 RPM	25.82 RPM
SRP030211_testis	1.11 RPM	28.19 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1106 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1106 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006296	1 retrocopy	retro_btau_1106 ,
Callithrix jacchus	ENSCJAG00000003916	1 retrocopy	retro_cjac_150,
Dasypus novemcinctus	ENSDNOG00000008426	1 retrocopy	retro_dnov_504,
Homo sapiens	ENSG00000160131	1 retrocopy	retro_hsap_3724,
Macaca mulatta	ENSMMUG00000009034	1 retrocopy	retro_mmul_1693,
Mus musculus	ENSMUSG00000073131	2 retrocopies	retro_mmus_116, retro_mmus_3675,
Nomascus leucogenys	ENSNLEG00000013711	1 retrocopy	retro_nleu_1971,
Oryctolagus cuniculus	ENSOCUG00000015201	1 retrocopy	retro_ocun_443,
Pongo abelii	ENSPPYG00000020820	1 retrocopy	retro_pabe_3133,
Rattus norvegicus	ENSRNOG00000049744	1 retrocopy	retro_rnor_2843,
Ictidomys tridecemlineatus	ENSSTOG00000011179	1 retrocopy	retro_itri_500,