RetrogeneDB ID: retro_cjac_4121

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:117763843..117764070(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLE3
• Ensembl ID: ENSCJAG00000017917
• Aliases: None
• Description: polymerase (DNA directed), epsilon 3, accessory subunit [Source:HGNC Symbol;Acc:13546]

Sequence

>retro_cjac_4121
CAGAAGCCCAAAGACCTAAACCTGCCCAATGCCAGCATCACCAGGATCAACAAGGAGGCGCTCCTGGACAATGTCAGCAT
CTCCAAGGAGGCCCGGAGCGCCATCTCCCACGCCGCCAGCATCTTGGTGCTATACACGACATCCTGTGCCAACAACTTGG
CAATGAAAGGAAAGTGCAAGACGCTGATGTGCTTTCAGCCATGGAAGAGATGGAGTTCCAGCAATTC

Alignment

ORF - retro_cjac_4121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.23 %
• Parental protein coverage: 51.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERPEDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTL-NATDVLS
          ..P.DLNLPNA.ITRI.KEAL.D.V.ISKEARSAIS.AAS..VLY.TSCANN.AMKGK.KTL........
Retrocopy QKPKDLNLPNASITRINKEALLDNVSISKEARSAISHAASILVLYTTSCANNLAMKGKCKTL<DVLSAME

Parental  AMEEMEF
          .ME...F
Retrocopy EMEFQQF

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	17.11 RPM
SRP051959_heart	0.00 RPM	11.47 RPM
SRP051959_kidney	0.00 RPM	17.44 RPM
SRP051959_liver	0.00 RPM	11.85 RPM
SRP051959_lung	0.00 RPM	15.32 RPM
SRP051959_lymph_node	0.00 RPM	15.07 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.47 RPM
SRP051959_spleen	0.00 RPM	19.73 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4121 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4121 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4121 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014610	1 retrocopy	retro_cjac_1133,
Callithrix jacchus	ENSCJAG00000017917	1 retrocopy	retro_cjac_4121 ,
Cavia porcellus	ENSCPOG00000000313	1 retrocopy	retro_cpor_355,
Dipodomys ordii	ENSDORG00000003073	2 retrocopies	retro_dord_526, retro_dord_652,
Monodelphis domestica	ENSMODG00000004358	3 retrocopies	retro_mdom_1680, retro_mdom_1920, retro_mdom_647,
Mus musculus	ENSMUSG00000028394	2 retrocopies	retro_mmus_124, retro_mmus_555,
Pteropus vampyrus	ENSPVAG00000004717	1 retrocopy	retro_pvam_302,
Rattus norvegicus	ENSRNOG00000015392	1 retrocopy	retro_rnor_55,
Ictidomys tridecemlineatus	ENSSTOG00000027365	1 retrocopy	retro_itri_866,
Tupaia belangeri	ENSTBEG00000005211	1 retrocopy	retro_tbel_4052,