RetrogeneDB ID: retro_btau_1667

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:14237088..14237425(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9H12orf49
• Ensembl ID: ENSBTAG00000047139
• Aliases: C9H12orf49, C12orf49
• Description: UPF0454 protein C12orf49 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q17QN8]

Sequence

>retro_btau_1667
GTTTGGGAGAGGAAAGATTTGCTGGTGAATGGCTGCTGTAACCTCAACGTCCCTGGCACGAAGCAGTACTGCTGTGATGG
CTGCTCGTCCAGTGGCCGCTGTAGTGCCCAGGAGTACTGTGTCTCCTGCTGCCTGCCGCCCGACAAGCAACTACTCCTGG
AGCGCTTCTTTAGACGTGCAGCCGTGGCATTCCAGAACCTCTTCATGGCATTTGAAGTTATCTTTGAATTGTGTTTGGCT
AAACGCAGAGCATAATCCCAGAGCATGCAGCGTGGATCCTATAGGATCCCATAGCAAAGACTGCTATGGAGAGAGCCCTC
CCAAGCTCTTCCTGGCA

Alignment

ORF - retro_btau_1667 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.59 %
• Parental protein coverage: 55.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VCERRDLLVNGCCNVNVPGTKQYCCDGCLSSGCCSAYEYCVSCCLQPNKQLLLERFLNRAAVAFQNLFMA
          V.ER.DLLVNGCCN.NVPGTKQYCCDGC.SSG.CSA.EYCVSCCL.P.KQLLLERF..RAAVAFQNLFMA
Retrocopy VWERKDLLVNGCCNLNVPGTKQYCCDGCSSSGRCSAQEYCVSCCLPPDKQLLLERFFRRAAVAFQNLFMA

Parental  VEDHFELCLAKCRTSSQSVQHENTYR-DPIAKY-CYGESPPELFPA
          .E..FELCLAK.R..SQS.Q....YR.DPIAK..CYGESPP.LF.A
Retrocopy FEVIFELCLAKRRA*SQSMQ-RGSYR<DPIAKT<CYGESPPKLFLA

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	6.56 RPM
ERP005899_muscle	0.00 RPM	21.49 RPM
SRP017611_brain	0.00 RPM	20.01 RPM
SRP017611_kidney	0.00 RPM	15.06 RPM
SRP017611_liver	0.00 RPM	13.29 RPM
SRP030211_testis	0.03 RPM	24.40 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1667 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1667 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1667 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012481	2 retrocopies	retro_amel_1518, retro_amel_1578,
Bos taurus	ENSBTAG00000047139	1 retrocopy	retro_btau_1667 ,
Callithrix jacchus	ENSCJAG00000009570	1 retrocopy	retro_cjac_1471,
Dasypus novemcinctus	ENSDNOG00000001294	9 retrocopies	retro_dnov_126, retro_dnov_1532, retro_dnov_1609, retro_dnov_1622, retro_dnov_1739, retro_dnov_2042, retro_dnov_2185, retro_dnov_2285, retro_dnov_232,
Echinops telfairi	ENSETEG00000016892	3 retrocopies	retro_etel_1064, retro_etel_1377, retro_etel_410,
Homo sapiens	ENSG00000111412	1 retrocopy	retro_hsap_4758,
Gorilla gorilla	ENSGGOG00000015690	2 retrocopies	retro_ggor_2963, retro_ggor_508,
Myotis lucifugus	ENSMLUG00000011912	1 retrocopy	retro_mluc_166,
Macaca mulatta	ENSMMUG00000018247	2 retrocopies	retro_mmul_2376, retro_mmul_2537,
Pan troglodytes	ENSPTRG00000005500	1 retrocopy	retro_ptro_2798,