RetrogeneDB ID: retro_btau_490

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:24696460..24697004(-)
• Located in intron of: ENSBTAG00000011860

Retrocopy information

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

Parental gene information

• Parental gene symbol: C3H1orf146
• Ensembl ID: ENSBTAG00000027936
• Aliases: C3H1orf146, C1orf146
• Description: None

Sequence

>retro_btau_490
ATGGCTGAAAGTTGATGGAAAAGGAAAAATAAAATGGACAACCACCATTATTATTAGCTCATCTCTTAAGAGTTATGAAG
TTGCAGCTGCTCTAGAAAATCGAAGCCACAAGGTTCAGTATTCAGATTCAGTGGAAAATGGATCAATTATATTTTCTCTT
TCTGGAGTTGCATTTTTATTGATGGATGCTAGAGAATGCTTTATGTCTGCTAAAGAAACATTTCTAGCCAAAATTGAGAA
GTTTATTAACATCTACCAAAATAGTTTTTTGGTTCTGTCTGCTGCCCTGCATGGACCTGAAGAATGGAAACTGATGTTCA
GGATTCAGCAGAGATTCCTGGGTAGTAACTTATGGATACTTCCAGTACACAACACAGTAAATACGATTAACCTTATGTGC
ACCATAGCTAAGATCACCTCCAAATCATACATAGATAGCATCTGCTACAGAATGATAACAACTAAAGCTTACATCATTGA
GCAAAGTCCTGTGTGGAAAACACTTCAAAAGATAAAACTGAGTAGTGATACATTTAACCCAAAT

Alignment

ORF - retro_btau_490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAES-DGKEKIKWTTTIIISSSLKSYEVAAALENRSHKVRYSDSVENGSIIFSLSGVAFLLMDARECFMS
          MAES.DGK.KIKWTTTIIISSSLKSYEVAAALENRSHKV.YSDSVENGSIIFSLSGVAFLLMDARECFMS
Retrocopy MAES>DGKGKIKWTTTIIISSSLKSYEVAAALENRSHKVQYSDSVENGSIIFSLSGVAFLLMDARECFMS

Parental  AEETFLAKIEKFINIHQNSFLVLFAALHGPEEWKLMFRIQQRFLGSNLRILPVHNTVNAINLMCTIAKIT
          A.ETFLAKIEKFINI.QNSFLVL.AALHGPEEWKLMFRIQQRFLGSNL.ILPVHNTVN.INLMCTIAKIT
Retrocopy AKETFLAKIEKFINIYQNSFLVLSAALHGPEEWKLMFRIQQRFLGSNLWILPVHNTVNTINLMCTIAKIT

Parental  SKSYIDSICYRMITTKAYIIEQSPVWKTLQKIKLSSDTFNPN
          SKSYIDSICYRMITTKAYIIEQSPVWKTLQKIKLSSDTFNPN
Retrocopy SKSYIDSICYRMITTKAYIIEQSPVWKTLQKIKLSSDTFNPN

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	1.51 RPM	0.14 RPM
ERP005899_muscle	1.48 RPM	0.11 RPM
SRP017611_brain	0.09 RPM	0.27 RPM
SRP017611_kidney	0.83 RPM	0.30 RPM
SRP017611_liver	0.08 RPM	0.00 RPM
SRP030211_testis	0.27 RPM	7.56 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_490 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_490 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_490 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027936	1 retrocopy	retro_btau_490 ,
Choloepus hoffmanni	ENSCHOG00000004012	1 retrocopy	retro_chof_2167,
Callithrix jacchus	ENSCJAG00000017547	1 retrocopy	retro_cjac_1817,
Erinaceus europaeus	ENSEEUG00000003083	1 retrocopy	retro_eeur_601,
Homo sapiens	ENSG00000203910	1 retrocopy	retro_hsap_3381,
Gorilla gorilla	ENSGGOG00000006653	1 retrocopy	retro_ggor_2289,
Macropus eugenii	ENSMEUG00000013311	1 retrocopy	retro_meug_143,
Myotis lucifugus	ENSMLUG00000016984	1 retrocopy	retro_mluc_1260,
Macaca mulatta	ENSMMUG00000010094	1 retrocopy	retro_mmul_2107,
Nomascus leucogenys	ENSNLEG00000010426	1 retrocopy	retro_nleu_970,
Pongo abelii	ENSPPYG00000001156	1 retrocopy	retro_pabe_2780,
Pan troglodytes	ENSPTRG00000030530	1 retrocopy	retro_ptro_2298,
Ictidomys tridecemlineatus	ENSSTOG00000012506	1 retrocopy	retro_itri_404,
Tursiops truncatus	ENSTTRG00000014426	1 retrocopy	retro_ttru_1727,