RetrogeneDB ID: retro_rnor_2429

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:16880902..16881723(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pcgf6
• Ensembl ID: ENSRNOG00000020250
• Aliases: Pcgf6, Rnf134
• Description: Polycomb group RING finger protein 6 [Source:UniProtKB/Swiss-Prot;Acc:Q5XI70]

Sequence

>retro_rnor_2429
CCCCTGGAGTTGGAGCCAGAGCACAGTCTGGGCCTCTTGTGAGTCCACTTCGAGAACTATGATGAGGAGTTGGAAGAAGA
TTAGGAGATGGAGGAGGAGAAAGACCAGGAGGAAGAGATGAGCCACTTCTCTCTGAGTCTGGAGTCCGGATGTGCAAACT
CCTAGGACCAGGAGAAGAGCCTGATGAACCTGACTGAGCTGACGCCCTACATCTTGTGCTCCATTCGCAAAGGTTAATTG
ATACATGCCACCACTATTGCAGAATGTCTCCACACCTTTTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGCAACAG
ATGCCCCAAATGCAACATAGTAGTCCACCAGACTCAGCCTCTTTATAATATAAGGTTGGACCGGCAGTTACAAGACAAAG
TATATAAATTAGTAATCAATCTAGCGGAAAGAGGAAAAAAGCAAAAGCACGACTTCTATAAAGAAAGAGGTCTAGAAGTC
CCTAAGCCTGCTCTTACACAGCCAGTCGCTGCAAACAAAGGAAGAACCCAGAAAATCCTAGAGTCAGTGTTTTGTATTCC
ACCTGATGTTTTATTGATGTTGAGTTCATTGATGCTAATGAAGACAGAGGACATTTTAAGCCATTGGAAAAGAAGTTTGT
GCATGTTTCAGGAGAAGCAACTACTGGGTATGTAGAAAAATTTCTTGGAAGAAAATTGTGTCTTGATCCAGCTTGTCAGG
TAGATAACATCTGTGGGGATCACTTATTGGAGCGGTACCAAACTCTGCAGGAAATCCGATGTTCAATACGTGACACAGCA
ATGCAGGATGGTCTACCTGTT

Alignment

ORF - retro_rnor_2429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.14 %
• Parental protein coverage: 78.63 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPELEPERSLGRLRGRFEDYDEELEEDEEMEEEEEEEEEMSHFSLRLESGRADSEDEEERLINLVELTPY
          P.ELEPE.SLG.L...FE.YDEELEED.EMEEE...EEEMSHFSL.LESG.A.S.D.E..L.NL.ELTPY
Retrocopy PLELEPEHSLGLL*VHFENYDEELEED*EMEEEKDQEEEMSHFSLSLESGCANS*DQEKSLMNLTELTPY

Parental  ILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLYNIRLDRQLQDIVYKLVVN
          ILCSI.KG.LI.ATTI.ECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLYNIRLDRQLQD.VYKLV.N
Retrocopy ILCSIRKG*LIHATTIAECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLYNIRLDRQLQDKVYKLVIN

Parental  LEEREKKQMHDFYKERGLEVPKPAVPQPVPASKGRTKKALESVFRIPPELDVSLLL-EFIGANEDTGHFK
          L.ER.KKQ.HDFYKERGLEVPKPA..QPV.A.KGRT.K.LESVF.IPP..DV.L.L.EFI.ANED.GHFK
Retrocopy LAERGKKQKHDFYKERGLEVPKPALTQPVAANKGRTQKILESVFCIPP--DVLLML<EFIDANEDRGHFK

Parental  PLEKKFVRVSGEATIGHVEKFLRRKMGLDPACQVDIICGDHLLERYQTLREIRRAIGDTAMQDGLLV
          PLEKKFV.VSGEAT.G.VEKFL.RK..LDPACQVD.ICGDHLLERYQTL.EIR..I.DTAMQDGL.V
Retrocopy PLEKKFVHVSGEATTGYVEKFLGRKLCLDPACQVDNICGDHLLERYQTLQEIRCSIRDTAMQDGLPV

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	11.29 RPM
SRP017611_kidney	0.00 RPM	6.28 RPM
SRP017611_liver	0.00 RPM	7.06 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2429 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2429 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000004417	1 retrocopy	retro_etel_707,
Myotis lucifugus	ENSMLUG00000004985	1 retrocopy	retro_mluc_815,
Rattus norvegicus	ENSRNOG00000020250	2 retrocopies	retro_rnor_2429 , retro_rnor_2430,