RetrogeneDB ID: retro_cjac_2026

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:19437998..19438522(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2C
• Ensembl ID: ENSCJAG00000012016
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Source:HGNC Symbol;Acc:9189]

Sequence

>retro_cjac_2026
CAGTGCTTGGTGGAGTTTACCCTCAGTGCGCAGTGCAATGAAGACCAGATTCAACATGTCACGTCTTGAGACCTCATCTC
CAACAGCCCCCAGGTCATTCTGGTGACATCCCACAACCAAGATAATGAACTAATGACTATATGGAGCAGGATGACATTCT
CATCATCAAGTTGAGAAAGGGCCAGGAGCTGAGACTTTGAGCCTATGCCAAAAAGTGCTTTGGCAAGGAGCATGCCAAGT
TGAACCCTACTGCAGGGGTGGCTTTTGAATACAATCCAGACAATGCCCTGAGGCATGCAGTGTACCCCAAACCCAAGGAA
TGGACAAAGAGTGAGCGAGCACCTGGAGCTGCATGAGGATGAATCACAGGATTTTTGCCCTGTGACCCCAAGGGCAAGCC
AGAGAGGTTTTACTGCAATGCAAAGTCCTATGGCTCTCTGTGTCCTGGAACCATTGTCCTCTCAGCTCTTTCTGCATTGA
AGAAGAAGCTGAGTGATTTACAAACTCAACTAAGCCATGAGATC

Alignment

ORF - retro_cjac_2026 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.47 %
• Parental protein coverage: 62.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSRNRDND-PNDYVEQDDILIVKLRKGQELRLRAY
          .C.VEFTL...CNEDQ..HVTS.DLISNSP.VI.VTS.N.DN...NDY.EQDDILI.KLRKGQELRL.AY
Retrocopy QCLVEFTLSAQCNEDQIQHVTS*DLISNSPQVILVTSHNQDNE<TNDYMEQDDILIIKLRKGQELRL*AY

Parental  AKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVY-PKPEEWPK-SEYSEL--DEDESQAPY-DPNGKPERF
          AKK.FGKEHAK.NPTAGVAFEY.PDNALRH.VY.P.P......SE..EL..DE.....P..DP.GKPERF
Retrocopy AKKCFGKEHAKLNPTAGVAFEYNPDNALRHAVY>PNPRNGQRVSEHLELHEDESQDFCPV<DPKGKPERF

Parental  YYNVESCGSLRPETIVLSALSGLKKKLSDLQTQLSHEI
          Y.N..S.GSL.P.TIVLSALS.LKKKLSDLQTQLSHEI
Retrocopy YCNAKSYGSLCPGTIVLSALSALKKKLSDLQTQLSHEI

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	11.34 RPM
SRP051959_heart	0.00 RPM	18.52 RPM
SRP051959_kidney	0.07 RPM	20.83 RPM
SRP051959_liver	0.00 RPM	21.25 RPM
SRP051959_lung	0.00 RPM	13.94 RPM
SRP051959_lymph_node	0.02 RPM	16.87 RPM
SRP051959_skeletal_muscle	0.02 RPM	21.84 RPM
SRP051959_spleen	0.00 RPM	14.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2026 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2026 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2026 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2496
Pan troglodytes	retro_ptro_1448
Gorilla gorilla	retro_ggor_1557
Pongo abelii	retro_pabe_1839

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008720	1 retrocopy	retro_cfam_688,
Choloepus hoffmanni	ENSCHOG00000002986	1 retrocopy	retro_chof_1988,
Callithrix jacchus	ENSCJAG00000012016	1 retrocopy	retro_cjac_2026 ,
Dipodomys ordii	ENSDORG00000000081	1 retrocopy	retro_dord_704,
Echinops telfairi	ENSETEG00000004185	1 retrocopy	retro_etel_1953,
Homo sapiens	ENSG00000102978	1 retrocopy	retro_hsap_2496,
Gorilla gorilla	ENSGGOG00000012415	1 retrocopy	retro_ggor_1557,
Myotis lucifugus	ENSMLUG00000015833	2 retrocopies	retro_mluc_129, retro_mluc_236,
Macaca mulatta	ENSMMUG00000020474	1 retrocopy	retro_mmul_1674,
Mus musculus	ENSMUSG00000031783	1 retrocopy	retro_mmus_1723,
Nomascus leucogenys	ENSNLEG00000003034	1 retrocopy	retro_nleu_1431,
Otolemur garnettii	ENSOGAG00000016866	1 retrocopy	retro_ogar_3361,
Ochotona princeps	ENSOPRG00000006979	1 retrocopy	retro_opri_445,
Pongo abelii	ENSPPYG00000007390	1 retrocopy	retro_pabe_1839,
Pan troglodytes	ENSPTRG00000008157	1 retrocopy	retro_ptro_1448,