RetrogeneDB ID: retro_cjac_3885

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285806.1:20751..22658(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000000717
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POLR3E
• Ensembl ID: ENSCJAG00000008918
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide E (80kD) [Source:HGNC Symbol;Acc:30347]

Sequence

>retro_cjac_3885
AGAAGCAAAGGGGAGCAGATTGAGCTGAACGTGGACGGGGCCTGCGTGGATGAGACCAGCACGTACTCCTCGAAGCTGAT
GGACAAGCAGACCTTCTGCTCTTCCCAGACCACCAGGAACACATCCCATTACGCCGCTGCACTCTACAGGCAAGGTGAGC
TCTACCTGACACCTTCACATGGCATTTTGCAGCTGCGGCCCAGCTTCTCCTACCTGGATAAGGCGGACGCCAAGCACCGG
GAGAGGGAGGCAGGCGATGAAGCAGGGGACTCTTCACAGGATGAGGTGGAAGACGATGTTAAGCAGATCACGGTGGGGTC
CTCGCGGCCCGAGTCACGCAGGCCCCCGCGCCGCTTGTCCTATGAGTTCCTGCAGAAGAAGCATGCGCAGGAGGCCTGGG
TCCACCTGCATTACTATGGCCTGAAGGACAGCCGCTCTGAGCACGAGCGCCAGTACCTGCTATGCCCAGGCTCGAGCGGG
GAGGAGAACACAGAGCTTGTCAAGTCACCCAGTGAGTACCTGTTGATGCTGATGCCGCCCAGCCAGGAGGAGGAGAAAGA
CAAGCCTGTGGCCTCCAGCAACGTCCTGTCCATGGCCCCGCTGCGCACGCTGCCCCTGGCCGGTCAGATCAAGATCCTGA
TGAAGAACGTGAAGGCCATGCCTTTGGCCAACTTGATGAGCCTCCTGGGCCCCGCCATCGATTCCGTGGCTGTTCTGCGC
GGCATCCAGAAGGTGGCGATGTTGGTCCAAGGGAGCCCGGTGGTGAAGCGTGACATCCTGTGCTCCAAGGACTTATCCAG
CCGTCACAGCGGCGTGCCCGTGCCCGCCGGAGTGCTCTGCGGCGGCTGAGACTTCGTTATGCGGAAGTTCACGCAGAGCC
GCTGGGTGGTTAGGAACGAGGTGGCAACAGTGACCAAACTCTGCACCGGGGACGTGAAGGACTTCCTGGAGCACGTGGCC
GTGGTGAGGATCAACAACGGCTGGGAGTTCATTCTGCCTTAGGACGGGGAGTTCATCAGAAAGCACCGGGATGCGGTCCA
GCGGCAGCACCTGCTGTGGACGGGTATCCGGGCCACACTGGAAAAAGTCTATAATCCTGTAAAGGAAACCAGGCCAAAGA
AGCCGGATGCACAATCAGGGCCTGCCGGGCTGGTCTCTGGGGACCAGCGGATCCAAGTAGCCAAAACCAAGGCCCGGCAG
AACCACGCGTTGCTGGAGCGGGAACTGCAGCGGCGGAAGGAGCAGCTGCGGGCGCCTGTGGTCCAGCCGGGTGTGCGGAT
CAAGGAGGAGCCAGTGAGGGGGGAGGGCGAGGACGATGACGAGGAGGAGGAGCCCGTGGACACTTGCCCCAGCGGCGGCC
TCCACAGCAGGCTGACCAACGGGCTGCCTCCCGGGCGGGCTTCGGGCACGGACAGCTTCAACGGGCATCCGCCCTCGGGC
TGTGCTAGCACCCCCGTGACCGGGGAACTGAGCGCCTTTGGGAAGGCCACCTTTCAGAGACAGTTTGTGTTCACGCTGAG
TGAAATCCAGCTCCTCTTCAACCTGCACATGGCCAGCCTGCCCCCGGCCACAGGCTCTTCAGTGGCAACTTGGACCGCAT
GCTGCGGGACACGGTGTTGGACGCTTGTTGCAGGGAGATACTGGTACCTTTTCCCACGCAGACTGCTGCTACCCCGGATG
AGCAGAAAGTGTTTGCCCTCTGGGAGTCTGGAGGTACGAGCGATCAGCATCGAAGGGTTTTGATTGAAATGTTTTCCAAA
AATTACCGAGTACGCCGAAGCATGATCCAGTCTCGGTTGACTCAAGAGTGTGGAGAAGATCTCAGTAAACAGGAGGTGGA
TAAAGTACTGAAGGCCTGCTGTGTAAGCTATGGTGGCAGGTGGTACCTTCAAGGGACAGTACAGTCT

Alignment

ORF - retro_cjac_3885 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 90.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSKGEQIALNVDGACADETSTYSSKLMDKQTFCSSQTTSNTSRYAAALYRQGELHLTPLHGILQLRPSFS
          RSKGEQI.LNVDGAC.DETSTYSSKLMDKQTFCSSQTT.NTS.YAAALYRQGEL.LTP.HGILQLRPSFS
Retrocopy RSKGEQIELNVDGACVDETSTYSSKLMDKQTFCSSQTTRNTSHYAAALYRQGELYLTPSHGILQLRPSFS

Parental  YLDKADAKHREREAANEAGDSSQDEAEDDVKQITVRFSRPESEQARQRRVQSYEFLQKKHAEEAWVHLHY
          YLDKADAKHREREA..EAGDSSQDE.EDDVKQITV..SRPES.....R...SYEFLQKKHA.EAWVHLHY
Retrocopy YLDKADAKHREREAGDEAGDSSQDEVEDDVKQITVGSSRPESRRPPRRL--SYEFLQKKHAQEAWVHLHY

Parental  YGLKDSRSEHERQYLLCPGSSGVENTELVKSPSEYLLMLMPPSQEEEKDKPVAPSNVLSMAQLRTLPLAD
          YGLKDSRSEHERQYLLCPGSSG.ENTELVKSPSEYLLMLMPPSQEEEKDKPVA.SNVLSMA.LRTLPLA.
Retrocopy YGLKDSRSEHERQYLLCPGSSGEENTELVKSPSEYLLMLMPPSQEEEKDKPVASSNVLSMAPLRTLPLAG

Parental  QIKILMKNVKVMPFANLMSLLGPSIDSVAVLRGIQKVAMLVQGNWVVKSDILYPKDSSSPHSG--VPAEV
          QIKILMKNVK.MP.ANLMSLLGP.IDSVAVLRGIQKVAMLVQG..VVK.DIL..KD.SS.HSG..VPA.V
Retrocopy QIKILMKNVKAMPLANLMSLLGPAIDSVAVLRGIQKVAMLVQGSPVVKRDILCSKDLSSRHSGVPVPAGV

Parental  LCRGRDFVMWKFTQSRWVVRKEVATVTKLCTEDVKDFLEHMAVVRINKGWEFILPYDGEFIKKHPDVVQR
          LC.G.DFVM.KFTQSRWVVR.EVATVTKLCT.DVKDFLEH.AVVRIN.GWEFILP.DGEFI.KH.D.VQR
Retrocopy LCGG*DFVMRKFTQSRWVVRNEVATVTKLCTGDVKDFLEHVAVVRINNGWEFILP*DGEFIRKHRDAVQR

Parental  QHMLWTGIQAKLEKI----KETMPKKLDAQSGPAGLVSGDQRIQVAKTKAQQNHALLERELQWRKEQLRA
          QH.LWTGI.A.LEK.....KET.PKK.DAQSGPAGLVSGDQRIQVAKTKA.QNHALLERELQ.RKEQLRA
Retrocopy QHLLWTGIRATLEKVYNPVKETRPKKPDAQSGPAGLVSGDQRIQVAKTKARQNHALLERELQRRKEQLRA

Parental  PAVPPGVRIKEEPVSEEGEDDDDEEEEPMETSPSGGVHSRLANGLPPGRAAGTDSFNGHLPPGCASTPMA
          P.V.PGVRIKEEPV..EGE.DDDEEEEP..T.PSGG.HSRL.NGLPPGRA.GTDSFNGH.P.GCASTP..
Retrocopy PVVQPGVRIKEEPVRGEGE-DDDEEEEPVDTCPSGGLHSRLTNGLPPGRASGTDSFNGHPPSGCASTPVT

Parental  RELRAFVEATFQRQFVLTLSELKRLFNLHLASLP-PGHTLFSGISDRMLQDTVLAAGCKQILVPFPPQTA
          .EL.AF..ATFQRQFV.TLSE...LFNLH.ASLP.PGH.LFSG..DRML.DTVL.A.C..ILVPFP.QTA
Retrocopy GELSAFGKATFQRQFVFTLSEIQLLFNLHMASLP<PGHRLFSGNLDRMLRDTVLDACCREILVPFPTQTA

Parental  ASPDEQKVFALWESGDMSDQHRQVLLEIFSKNYRVRRNMIQSRLTQECGEDLSKQEVDKVLKDCCVSYGG
          A.PDEQKVFALWESG..SDQHR.VL.E.FSKNYRVRR.MIQSRLTQECGEDLSKQEVDKVLK.CCVSYGG
Retrocopy ATPDEQKVFALWESGGTSDQHRRVLIEMFSKNYRVRRSMIQSRLTQECGEDLSKQEVDKVLKACCVSYGG

Parental  MWYLKGTVQS
          .WYL.GTVQS
Retrocopy RWYLQGTVQS

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
SRP051959_colon	0.02 RPM	9.87 RPM
SRP051959_heart	0.00 RPM	11.16 RPM
SRP051959_kidney	0.00 RPM	11.80 RPM
SRP051959_liver	0.00 RPM	7.84 RPM
SRP051959_lung	0.05 RPM	13.40 RPM
SRP051959_lymph_node	0.05 RPM	16.69 RPM
SRP051959_skeletal_muscle	0.00 RPM	18.15 RPM
SRP051959_spleen	0.02 RPM	11.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3885 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3885 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3885 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008918	2 retrocopies	retro_cjac_3734, retro_cjac_3885 ,
Equus caballus	ENSECAG00000015801	1 retrocopy	retro_ecab_144,