RetrogeneDB ID: retro_btau_530

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:50193478..50194109(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM17
• Ensembl ID: ENSBTAG00000021951
• Aliases: None
• Description: splicing factor 45 [Source:RefSeq peptide;Acc:NP_001094553]

Sequence

>retro_btau_530
GAGCAACAAATAGGGGACCCCCCACCACACATGACCACGGGCATCAACGACCGTTTCCAGCCAGTTTTCTGCAGGATAAG
TGTTTATCCCCTCAGCTGATGTATAGGATCCCATGTTTCCTAATGATTATAAGAAAGTAGTGAAGCACCAAAGAGAAGAG
CAACAGAGACAGCAAGAACTGGAAAGACAGAAGGAAACAGAAGAGAGAGAAAAAAGGCATAAATAGACATGAAGCTAGTG
GATTTTCCAGGTGCACCAGATCCAGATTCTGTTGAAGATGTAGATTATGAGTGAGAGAGGAGGAAAAGAATAAGGGCGGA
GCCACCATCACACCCCGCCACGTCTCTTGTGGAGAAGGACAGAGTTACCCCAAGACGTCCCTTATGAAGAGGATTCGCCA
CCTCGCTCACAGTCTTCCAAAGTTTCTATCCCTTCCACAGTGTACAAGGAATAGGACAGACTGCGATCCCAGACAACCAG
CATTGGCAACTCTTTCCTCGCCAACATGGGGGGCAGGGTAGTACATAAATTTATGCAGAAATAAGGCTTCTGGGAAGGCC
AGGGTATCAGGAAGCAAGAGCAGGGTCTGAGCACAGCACCATCAGTGGAGAAGACCACCAAGTGGGGAGGC

Alignment

ORF - retro_btau_530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.84 %
• Parental protein coverage: 52.62 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ERQIVDTPPHVAAGLKD-PVP-SGFSAGEVLIPLADEYDPMFPNDYEKVVKRQREERQ-RQRELERQKEI
          E.QI.D.PPH...G..D.P.P.S.FSAG.V.IP.AD..DPMFPNDY.KVVK.QR.E.Q.R..........
Retrocopy EQQIGDPPPHMTTGIND<PFP<SQFSAG*VFIPSADV*DPMFPNDYKKVVKHQR-EEQ>RDSKNWKDRRK

Parental  EEREKRRKDRHEASGFSR-RPDPDSDEDEDYERERRKR-SMGGAAIAP-PTSLVEKDKELPRDFPYEEDS
          ..REK....RHEASGFSR..PDPDS.ED.DYE.ERRKR...GGA.I.P.P..L.....ELP.D.PYEEDS
Retrocopy QKREKKGINRHEASGFSR>APDPDSVEDVDYE*ERRKR<NKGGATITP<PPRLLWRRTELPQDVPYEEDS

Parental  RPRSQSSKAAIPPPVYEEQDRPRSPTGP-GNSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSV
          .PRSQSSK..IP..VY.E.DR.RS.T...GNSFLANMGG.V.HK.MQK.GF.EGQG..K.EQGLSTA.SV
Retrocopy PPRSQSSKVSIPSTVYKE*DRLRSQTTSIGNSFLANMGGRVVHKFMQK*GFWEGQGIRKQEQGLSTAPSV

Parental  EKTSKRGG
          EKT.K.GG
Retrocopy EKTTKWGG

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	16.80 RPM
ERP005899_muscle	0.00 RPM	23.65 RPM
SRP017611_brain	0.00 RPM	36.63 RPM
SRP017611_kidney	0.00 RPM	32.30 RPM
SRP017611_liver	0.00 RPM	10.87 RPM
SRP030211_testis	0.00 RPM	57.31 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_530 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_530 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021951	2 retrocopies	retro_btau_1057, retro_btau_530 ,
Canis familiaris	ENSCAFG00000005206	1 retrocopy	retro_cfam_844,
Callithrix jacchus	ENSCJAG00000020573	1 retrocopy	retro_cjac_432,
Equus caballus	ENSECAG00000008939	1 retrocopy	retro_ecab_547,
Erinaceus europaeus	ENSEEUG00000013077	1 retrocopy	retro_eeur_390,
Homo sapiens	ENSG00000134453	1 retrocopy	retro_hsap_1551,
Macropus eugenii	ENSMEUG00000011347	1 retrocopy	retro_meug_438,
Macaca mulatta	ENSMMUG00000015152	2 retrocopies	retro_mmul_1209, retro_mmul_771,
Mus musculus	ENSMUSG00000037197	1 retrocopy	retro_mmus_2855,
Otolemur garnettii	ENSOGAG00000015687	1 retrocopy	retro_ogar_1119,
Pongo abelii	ENSPPYG00000002067	1 retrocopy	retro_pabe_1284,
Pan troglodytes	ENSPTRG00000002265	1 retrocopy	retro_ptro_1044,
Ictidomys tridecemlineatus	ENSSTOG00000013591	1 retrocopy	retro_itri_1376,
Tursiops truncatus	ENSTTRG00000001344	1 retrocopy	retro_ttru_1758,