RetrogeneDB ID: retro_cjac_2691

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:14101335..14102019(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023264
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POLR3G
• Ensembl ID: ENSCJAG00000010747
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide G (32kD) [Source:HGNC Symbol;Acc:30075]

Sequence

>retro_cjac_2691
ATGGCTGGGAATAAAGGAAGAGGACGTGCTGCTTATACCTTTAATATTGAAGCTGCTGGATTTAGCAAAGGTGAAAAGTT
ACCTGATGTAGTGTCGAAACCACCCCCACTATTTCCTGATACAGATTATAAACCAGTGACACTGAAAATGGGAGAAGGTG
AAGAATATATGCTGGCTTTGAAACAGGAGTTGAGAGAAACAATGAAAAGAATGCCTTATTTTATTGAAACACCTGAAGAA
AGACAAGATATTGAAAGGTATAGTAAAAGATATATGAAGGTGTACAAGGAAGAATGGATACCACATTGGAGAAGACTTCC
AAGAGAGATGATGCCAAGAAATAAATGTAAAAAAGGCCCCAAACCCAAAAAGGCAAAAGACGCAGGCAAAGGCACTTCAC
TCATTAATACTGCAGATGTTTTGAAAAACATTGAGGAATTGGAAAAGAGAGGTGATGGTGAAAAATCAGATGAGGAAAAT
GAAGAGAAAGAGGGAAGCAAAGAGAAAAGTAAAGAAGGCAAGGATGACAACGACCACGATGCTGCAGAACAGGACGAATA
TGATGAAGAAGACCAAGAAGAGGAAAATGACTACCTTAATTCATACTTTGGAGATGGAGATGACTTTGGCCCAGACAGGA
TGAAGCAAACTTTTAGGCATGAAATTAAAAAAAAAAAAATTTTA

Alignment

ORF - retro_cjac_2691 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.41 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGNKGRGRAAYTFNIEAVGFSKGEKLPDVVLKPPPLFPVTDYKPVPLKMGEGEEYMLALKQELRETMKR
          MAGNKGRGRAAYTFNIEA.GFSKGEKLPDVV.KPPPLFP.TDYKPV.LKMGEGEEYMLALKQELRETMKR
Retrocopy MAGNKGRGRAAYTFNIEAAGFSKGEKLPDVVSKPPPLFPDTDYKPVTLKMGEGEEYMLALKQELRETMKR

Parental  MSYFIETPEERQDIERYSKRYMKVYKEEWIPDWRRLPREMMPRNKCKKAGPKPKKAKDAGKGTSLTNTAD
          M.YFIETPEERQDIERYSKRYMKVYKEEWIP.WRRLPREMMPRNKCKK.GPKPKKAKDAGKGTSL.NTAD
Retrocopy MPYFIETPEERQDIERYSKRYMKVYKEEWIPHWRRLPREMMPRNKCKK-GPKPKKAKDAGKGTSLINTAD

Parental  VLKKIEELEKRGDGEKSDEENEDKEGSKEKSKEGEDDDDDDAAEQEEYDEEDQEEENDYINSYFEDGDDF
          VLK.IEELEKRGDGEKSDEENE.KEGSKEKSKEG.DD.D.DAAEQ.EYDEEDQEEENDY.NSYF.DGDDF
Retrocopy VLKNIEELEKRGDGEKSDEENEEKEGSKEKSKEGKDDNDHDAAEQDEYDEEDQEEENDYLNSYFGDGDDF

Parental  GADVMTTWMKQPIRHEIFKKIFL
          G.D.M....KQ..RHEI.KK..L
Retrocopy GPDRM----KQTFRHEIKKKKIL

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	2.42 RPM
SRP051959_heart	0.02 RPM	1.88 RPM
SRP051959_kidney	0.00 RPM	2.57 RPM
SRP051959_liver	0.00 RPM	4.68 RPM
SRP051959_lung	0.00 RPM	2.42 RPM
SRP051959_lymph_node	0.00 RPM	2.10 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.63 RPM
SRP051959_spleen	0.02 RPM	2.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2691 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2691 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2691 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006306	1 retrocopy	retro_chof_125,
Callithrix jacchus	ENSCJAG00000010747	1 retrocopy	retro_cjac_2691 ,
Echinops telfairi	ENSETEG00000008379	1 retrocopy	retro_etel_1040,
Homo sapiens	ENSG00000113356	2 retrocopies	retro_hsap_1454, retro_hsap_1885,
Gorilla gorilla	ENSGGOG00000000266	2 retrocopies	retro_ggor_1119, retro_ggor_1382,
Myotis lucifugus	ENSMLUG00000014954	1 retrocopy	retro_mluc_2233,
Macaca mulatta	ENSMMUG00000018972	1 retrocopy	retro_mmul_1332,
Nomascus leucogenys	ENSNLEG00000013749	1 retrocopy	retro_nleu_1807,
Otolemur garnettii	ENSOGAG00000005560	1 retrocopy	retro_ogar_3512,
Pongo abelii	ENSPPYG00000015624	1 retrocopy	retro_pabe_1564,
Pan troglodytes	ENSPTRG00000017068	2 retrocopies	retro_ptro_1266, retro_ptro_989,
Rattus norvegicus	ENSRNOG00000016260	2 retrocopies	retro_rnor_458, retro_rnor_503,
Ictidomys tridecemlineatus	ENSSTOG00000008664	1 retrocopy	retro_itri_18,
Tupaia belangeri	ENSTBEG00000002278	2 retrocopies	retro_tbel_2495, retro_tbel_3069,