RetrogeneDB ID: retro_btau_1015

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 23:49638871..49639396(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERI3
• Ensembl ID: ENSBTAG00000015559
• Aliases: ERI3, PRNPIP
• Description: ERI1 exoribonuclease 3 [Source:UniProtKB/Swiss-Prot;Acc:A6QLH5]

Sequence

>retro_btau_1015
GAGGAAATCATAGAGTTCCCCATCCTGAAGCTAAATGGCCGGACCATGGAGACTGAGTCTACTTTTCACACGTATGTCCA
GCCCGTAGTCCATCCACAGTGTACTCCCTTCTGTACAGAGCTCACTGGGATTATCCGAGCCATGGTGGATGGTCAGCCAA
GCCTGCAGCAAGTGCTGGAGAGGGGCGATGAGTGGACGGCGAAGAAAGGCCTCTTCGATCCAAACGTCAGGTGAATTTTT
GTCGCCTGTGGAGACTGGGACTTAAAAGTCATGCTCCCAGGACAGTGCCAGTACTGGGGCTTGCCAGTAGCAGATTACTT
CAAGCAGTGGATTAACCTGAAAAAGGCTTACAGCTTCGCCATGGGCTGCTGGCCCAAGAACGGACTTCTGGACATGAACA
AGGGCCTCGGCCTGCAATACACAGGCCGGCCCCACAGCGGCATTGATGACTGCAGGAACGTGGCCAACATCATGAAGACA
CTCGAGTGTTGAGGCTTCATCCTCAAGCAGGCGTCAAAGCCGTTC

Alignment

ORF - retro_btau_1015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.86 %
• Parental protein coverage: 51.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEG
          .EIIEFPILKLNGRTME.ESTFH.YVQPVVHPQ.TPFCTELTGII.AMVDGQPSLQQVLER.DEW.AK.G
Retrocopy EEIIEFPILKLNGRTMETESTFHTYVQPVVHPQCTPFCTELTGIIRAMVDGQPSLQQVLERGDEWTAKKG

Parental  LLDPNVKSIFVTCGDWDLKVMLPGQCQYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQH
          L.DPNV..IFV.CGDWDLKVMLPGQCQY.GLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGL.LQ.
Retrocopy LFDPNVR*IFVACGDWDLKVMLPGQCQYWGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLGLQY

Parental  IGRPHSGIDDCKNIANIMKTLAYRGFIFKQTSKPF
          .GRPHSGIDDC.N.ANIMKTL...GFI.KQ.SKPF
Retrocopy TGRPHSGIDDCRNVANIMKTLEC*GFILKQASKPF

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	8.58 RPM
ERP005899_muscle	0.00 RPM	22.65 RPM
SRP017611_brain	0.00 RPM	39.97 RPM
SRP017611_kidney	0.00 RPM	33.61 RPM
SRP017611_liver	0.00 RPM	9.36 RPM
SRP030211_testis	0.11 RPM	17.74 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1015 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1015 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1015 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015559	1 retrocopy	retro_btau_1015 ,
Callithrix jacchus	ENSCJAG00000003995	1 retrocopy	retro_cjac_3212,
Felis catus	ENSFCAG00000005285	1 retrocopy	retro_fcat_1768,
Pan troglodytes	ENSPTRG00000000655	1 retrocopy	retro_ptro_899,