RetrogeneDB ID: retro_btau_965

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 22:5574416..5574750(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C2H2orf76
• Ensembl ID: ENSBTAG00000010599
• Aliases: None
• Description: UPF0538 protein C2orf76 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q32KX9]

Sequence

>retro_btau_965
GTCAGCTCACTCGTGCATCACAATTTCAGACCTGCAGTGTATTATGGGCTTAATGTGGACCAAACTGCAGAATAATTTAC
AGTACTTCTGAAGCAAGATGCCCCTTTAAGGATCCACCTGCCACCACCACTCAGAAATTATAACTATGACAAACTAAAGA
TTATTCCTTGAGCACATAAACCAGAGACAAATGAACTTGTATTGGGTTTGGAAGACAACAGCAGACTCCCGTTAAAGGAA
GAGGCTCTCATAGCAGCTGGAATCACCACCGAGACTGAAACAGCATCTTCTTTGAAGAAGATTATAGAACTACAAAGCTA
ATCCCATTTCATCG

Alignment

ORF - retro_btau_965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.35 %
• Parental protein coverage: 89.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IRSFEHRNFRPVVYHGVHLDQTVKDFIVFLKQDIPLRASLPPPFRNYKYDKLKIVHQAHKSKTNELVLSL
          ..S..H.NFRP.VY.G...DQT...F.V.LKQD.PLR..LPPP.RNY.YDKLKI...AHK..TNELVL.L
Retrocopy VSSLVHHNFRPAVYYGLNVDQTAE*FTVLLKQDAPLRIHLPPPLRNYNYDKLKIIP*AHKPETNELVLGL

Parental  EDDDRLLLKEDSTLKAAGIASETEIA-FFCEEDYK-NYKANPISS
          ED..RL.LKE...L.AAGI..ETE.A..F.EEDY..NYKANPISS
Retrocopy EDNSRLPLKEEA-LIAAGITTETETA<IFFEEDYR<NYKANPISS

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	4.18 RPM
ERP005899_muscle	0.00 RPM	2.59 RPM
SRP017611_brain	0.00 RPM	2.42 RPM
SRP017611_kidney	0.00 RPM	4.33 RPM
SRP017611_liver	0.00 RPM	1.43 RPM
SRP030211_testis	0.00 RPM	14.25 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_965 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_965 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_965 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_1119
Equus caballus	retro_ecab_384

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008507	2 retrocopies	retro_amel_1062, retro_amel_1693,
Bos taurus	ENSBTAG00000010599	1 retrocopy	retro_btau_965 ,
Canis familiaris	ENSCAFG00000004896	2 retrocopies	retro_cfam_1119, retro_cfam_1727,
Equus caballus	ENSECAG00000002063	1 retrocopy	retro_ecab_384,
Myotis lucifugus	ENSMLUG00000004031	1 retrocopy	retro_mluc_1204,
Mustela putorius furo	ENSMPUG00000000943	1 retrocopy	retro_mputfur_726,
Mus musculus	ENSMUSG00000026388	1 retrocopy	retro_mmus_947,
Pteropus vampyrus	ENSPVAG00000011615	1 retrocopy	retro_pvam_337,
Sus scrofa	ENSSSCG00000015718	1 retrocopy	retro_sscr_311,