RetrogeneDB ID: retro_cjac_3734

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01197685.1:730..2068(-)
• Located in intron of: None

Retrocopy information

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

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_3734
AGAAGCAAAGGGGAGCAGATTGAGCTGAACGTGGACGGGGCCTGCGTGGATGAGACCAGCACGTACTCCTCTAAGCTGAT
GGACAAGCAGACCTTCTGCTCTTCCCAGACCACCAGGAACACATCCCATTACGCCGCTGCACTCTACAGGCAAGGTGAGC
TCTACCTGACACCTTCACATGGCATTTTGCAGCTGCGGCCCAGCTTCTCCTACCTGGATAAGGCGGACGCCAAGCACCGG
GAGAGGGAGGCAGGCGATGAAGCAGGGGACTCTTCACAGGATGAGGTGGAAGACGATGTTAAGCAGATCACGGTGGGGTC
CTCCCGGCCCGAGTCACAGCAGGCCCGCCAGCGCCGCGTGCAGTCCTATGAGTTCCTGCAGAAGAAGCATGCGCAGGAGG
CCTGGGTCCACCTGCATTACTATGGCCTGAAGGACAGCCGCTCTGAGCACGAGCGCCAGTACCTGCTATGCCCAGGCTCG
AGCGGGGAGGAGAACACAGAGCTTGTCAAGTCACCCAGTGAGTACCTGTTGATGCTGATGCCGCCCAGCCAGGAGGAGGA
GAAAGACAAGCCCGTGGCCTCCAGCAACGTCCTGTCCATGGCCCCGCTGCGCACGCTGCCCCTGGCCGGTCAGATCAAGA
TCCTGATGAAGAACGTGAAGGCCATGCCTTTGGCCAACTTGATGAGCCTCCTGGGCCCCGCCATCGATTCCGTGGCTGTT
CTGCGCGGCATCCAGAAGGTGGCGATGTTGGTCCAAGGGAGCCCGGTGGTGAAGCGTGACATCCTGTGCTCCAAGGACTT
ATCCAGCCGTCACAGCGGCGTGCCCGTGCCCGCCGGAGTGCTCTGCGGCGGCTGAGACTTCGTTATGTGGAAGTTCACGC
AGAGCCGCTGGGTGGTTAGGAACGAGGTGGCAACAGTGACCAAACTCTGCACCGGGGACGTGAAGGACTTCCTGGAGCAC
GTGGCCGTGGTGAGGATCAACAACGGCTGGGAGTTCATTCTGCCTTAGGACGGGGAGTTCATCAGAAAGCACCGGGATGC
GGTCCAGCGGCAGCACCTGCTGTGGACGGGTATCCGGGCCACACTGGAAAAAGTCTATAATCCTGTAAAGGAAACCAGGC
CAAAGAAGCCGGATGCACAATCAGGGCCTGCCGGGCTGGTCTCTGGGGACCAGCGGATCCAAGTAGCCAAAACCAAGGCC
CGGCAGAACCACGCGTTGCTGGAGCGGGAACTGCAGCGGCGGAAGGAGCAGCTGCGGGCGCCTGTGGTCCAGCCGGGTGT
GCGGATCAAGGAGGAGCCAGTGAGGGAGGAGGGCGAGGACGATGACGAGGAGGAGGAG

Alignment

ORF - retro_cjac_3734 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.44 %
• Parental protein coverage: 62.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

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

Parental  YLDKADAKHREREAANEAGDSSQDEAEDDVKQITVRFSRPESEQARQRRVQSYEFLQKKHAEEAWVHLHY
          YLDKADAKHREREA..EAGDSSQDE.EDDVKQITV..SRPES.QARQRRVQSYEFLQKKHA.EAWVHLHY
Retrocopy YLDKADAKHREREAGDEAGDSSQDEVEDDVKQITVGSSRPESQQARQRRVQSYEFLQKKHAQEAWVHLHY

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.DFVMWKFTQSRWVVR.EVATVTKLCT.DVKDFLEH.AVVRIN.GWEFILP.DGEFI.KH.D.VQR
Retrocopy LCGG*DFVMWKFTQSRWVVRNEVATVTKLCTGDVKDFLEHVAVVRINNGWEFILP*DGEFIRKHRDAVQR

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

Parental  PAVPPGVRIKEEPVSEEGEDDDDEEE
          P.V.PGVRIKEEPV.EEGEDDD.EEE
Retrocopy PVVQPGVRIKEEPVREEGEDDDEEEE

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	0.00 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	0.00 RPM	13.40 RPM
SRP051959_lymph_node	0.02 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_3734 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3734 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3734 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,