RetrogeneDB ID: retro_rnor_2074

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:155865499..155866097(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ppp6c
• Ensembl ID: ENSRNOG00000015145
• Aliases: None
• Description: Serine/threonine-protein phosphatase 6 catalytic subunit [Source:UniProtKB/Swiss-Prot;Acc:Q64620]

Sequence

>retro_rnor_2074
CAAGTATTCAGAACTGGAGTTAAGAGTCCCGACACGAACTGCACATTTATGGGTTAGTGTGTAGACAGAGGTTACTATAG
TTTGGAGTCCTTCACTCATCTTCTTGCAATAAAGCCTAAATGGCCTGGTTGTACTACATTTTTAAGAGGAAATTATGAGA
GTGGATAGGTAATTTAGGTGTGTGGGTTTTATGATGCGTGTCAAACCAAATATGGAAATGCTAATGCCTGGAGATGCTGT
ACTAAAGTTTCTGACATGCTCACAGTAGCAGCATTACTCGATGAGCAGATTTTGTATGTTCATAGCGTTTATCTCCTTGT
ATCAAAACACTGGATCAAATTCAAATCATTGAACAAATCAGGAAATCTCTTCCCCACTAAGGAGCTTTTGACCTGGCATG
ATCAGTACCTGAAGATGTAGAGACACTTTGGCAATCAGTTCCAAAGCTGGAGGGTAGCTTTTTTAAACCAAAGTTGCTAA
TGAGTTTGTTCATTTCAACTGTTTAAAATTCATCTTCAGAGCTCATGAGCTTGTACATGAAGACTGTAATTTTCTATGTG
ACAAGGATCTGGTCACAGTGAGATCTGCTCCTCACTAC

Alignment

ORF - retro_rnor_2074 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.02 %
• Parental protein coverage: 65.25 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELFRTGGQVPDTNYIFMGDFVDRGYYSLETFTYLLALKAKWPDRITLLRGNHESRQITQVYGFYDECQTK
          ..FRTG...PDTN..FMG..VDRGYYSLE.FT.LLA.K.KWP...T.LRGN.ES.....V.GFYD.CQTK
Retrocopy QVFRTGVKSPDTNCTFMG*CVDRGYYSLESFTHLLAIKPKWPGCTTFLRGNYESG*VI*VCGFYDACQTK

Parental  YGNANAWRYCTKVFDMLTVAALIDEQILCVHG-GLSPDIKTLDQIRTIER-NQEIPHKGAFCDLVWSDPE
          YGNANAWR.CTKV.DMLTVAAL.DEQIL.VH...LSP.IKTLDQI..IE......PH.GAF.DL..S.PE
Retrocopy YGNANAWRCCTKVSDMLTVAALLDEQILYVHS<RLSPCIKTLDQIQIIEQIRKSLPH*GAF-DLA*SVPE

Parental  DVDT-W-AISPRGAGWLFGAKVTNEFVHINNLKLICRAHQLVHEGYKFMFDEKLVTVWSAPNY
          DV.T.W.AIS....G.LF..KV.NEFVH.N.LK.I.RAH.LVHE...F..D..LVTV.SAP.Y
Retrocopy DVETLW<AISSKAGG*LF*TKVANEFVHFNCLKFIFRAHELVHEDCNFLCDKDLVTVRSAPHY

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
SRP017611_brain	0.00 RPM	29.98 RPM
SRP017611_kidney	0.00 RPM	46.20 RPM
SRP017611_liver	0.00 RPM	21.52 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2074 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2074 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2074 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012357	3 retrocopies	retro_chof_1759, retro_chof_183, retro_chof_608,
Dasypus novemcinctus	ENSDNOG00000015319	1 retrocopy	retro_dnov_1700,
Erinaceus europaeus	ENSEEUG00000010197	1 retrocopy	retro_eeur_706,
Macaca mulatta	ENSMMUG00000020549	1 retrocopy	retro_mmul_698,
Rattus norvegicus	ENSRNOG00000015145	1 retrocopy	retro_rnor_2074 ,
Sarcophilus harrisii	ENSSHAG00000008282	1 retrocopy	retro_shar_146,
Sus scrofa	ENSSSCG00000005600	1 retrocopy	retro_sscr_243,