RetrogeneDB ID: retro_btau_432

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:36050195..36050769(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF185
• Ensembl ID: ENSBTAG00000002828
• Aliases: None
• Description: RING finger protein 185 [Source:RefSeq peptide;Acc:NP_001077172]

Sequence

>retro_btau_432
ATGTTGAGCAAGGGGTCCTTGGCCTATGCGTCCCCTGAGAACTTGAGTGTTGGGGGCCCAGGGGCAGCAGCAGTGGTGCT
GGTGAGAGCAAAGGCCAGGATGGCACCTTGGAGTGCAGCATCTGCCTGGACACAGCCATGGAGGCCACCATCAGCCTGGG
CGGCCTCCTCTTCTCTTGGCCATGTTTACATCAGTGGCTGGAGACAAAACCTAACAGACAGGTGTGTCCCATTGGCAAAG
CTGGCCTCAGCAACAACAAAGTCATCCTGTTCCACAGCAGGGGCAGCCCTGGGCGGCAGGCCCCCAGAGAGCAGACCCCT
CCTCGCCCTCAAGGCCAGAGGCCAGAGCCGGAGAACAGAGGGGGATTCAAGGGTATGGATTTAGAGATGGTGGCTGCCAG
ATATATTTTGGAGTTGGGGTCTTTCCCTGTGGCATGTTTGCCACAGCATAGACCATGAACGATGGGTGGCCTCCTGCAGC
TGTCCTGGGAATGCCCCAGTATGTGGACAAGCAGTTTCTTTTATGCCCCTTCCTCTTTGCAGCACTGGTGATCATGTTCT
GGTTATTGATTGCC

Alignment

ORF - retro_btau_432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASKGPSAPASPDSSSAGGPS-GSSNGAGESGGQDSTFECNICLDTAKDAVISLCGHLFCWPCLHQWLET
          M.SKG..A.ASP...S.GGP..GSS.GAGES.GQD.T.EC.ICLDTA..A.ISL.G.LF.WPCLHQWLET
Retrocopy MLSKGSLAYASPENLSVGGPG<GSSSGAGESKGQDGTLECSICLDTAMEATISLGGLLFSWPCLHQWLET

Parental  RPNRQVCPVCKAGISRDKVIPLYGRGSTGQQDPREKTPPRPQGQRPEPENRGGF-QGFGFGDGGFQMSFG
          .PNRQVCP..KAG.S..KVI....RGS.G.Q.PRE.TPPRPQGQRPEPENRGGF.QG.GF.DGG.Q..FG
Retrocopy KPNRQVCPIGKAGLSNNKVILFHSRGSPGRQAPREQTPPRPQGQRPEPENRGGF<QGYGFRDGGCQIYFG

Parental  IGAFPFGIFATAFNINDGRPPPAVPGTPQYVDEQFLSRLFLFVALVIMFWLLIA
          .G.FP.G.FATA...NDG.PP.AV.G.PQYVD.QFL...FLF.ALVIMFWLLIA
Retrocopy VGVFPCGMFATA*TMNDGWPPAAVLGMPQYVDKQFLLCPFLFAALVIMFWLLIA

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	29.42 RPM
ERP005899_muscle	0.00 RPM	29.77 RPM
SRP017611_brain	0.00 RPM	30.70 RPM
SRP017611_kidney	0.00 RPM	57.26 RPM
SRP017611_liver	0.00 RPM	44.70 RPM
SRP030211_testis	0.00 RPM	66.90 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_432 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_432 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002828	1 retrocopy	retro_btau_432 ,
Cavia porcellus	ENSCPOG00000006556	1 retrocopy	retro_cpor_1051,