RetrogeneDB ID: retro_cjac_1087

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:38470780..38471113(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLE4
• Ensembl ID: ENSCJAG00000017156
• Aliases: None
• Description: None

Sequence

>retro_cjac_1087
TCAGGAAGCGGGACTCCCCGAAAGGAAGACGGACCCGCTAGGGAAGCAGCGGCCTCGCAGTCCCCAGCCCCAACTAGTGT
GCCTGGGGCACATCTCTCGAGGCTGCCTCTGGCGTGAGTAAACGCCTTGGTGAAGGCGGACCACGACGTGTCGCTAGCAG
GACAGGAAGCCATCTTCATTCTGGCACCAGCAGCGGAGCTATTTGTGGAGACCACTGCAAAAGATGCCTACTGCTGCGCT
CAGCAGGGAGAAAGGAAACCCCTTCAGAGGAGAGGCTTGGATAATGCAATAGAAGCTGTGGATGAATTTGCTTTTTTGGA
AGGTACTTTGGAT

Alignment

ORF - retro_cjac_1087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.49 %
• Parental protein coverage: 90.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGSGTPREEDGPAGEAAASQPPAPTTAPGARLSRLPLARVKALVKADPDVTLAGQEAIFILARAAELFVE
          SGSGTPR.EDGPA.EAAASQ.PAPT..PGA.LSRLPLA.V.ALVKAD.DV.LAGQEAIFILA.AAELFVE
Retrocopy SGSGTPRKEDGPAREAAASQSPAPTSVPGAHLSRLPLA*VNALVKADHDVSLAGQEAIFILAPAAELFVE

Parental  TIAKDAYCCAQQGKRKTLQRRDLDNAIEAVDEFAFLEGTLD
          T.AKDAYCCAQQG.RK.LQRR.LDNAIEAVDEFAFLEGTLD
Retrocopy TTAKDAYCCAQQGERKPLQRRGLDNAIEAVDEFAFLEGTLD

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	2.09 RPM
SRP051959_heart	0.00 RPM	2.68 RPM
SRP051959_kidney	0.02 RPM	3.22 RPM
SRP051959_liver	0.02 RPM	4.51 RPM
SRP051959_lung	0.00 RPM	3.81 RPM
SRP051959_lymph_node	0.00 RPM	6.12 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.90 RPM
SRP051959_spleen	0.00 RPM	3.80 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1087 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1087 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1087 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017073	1 retrocopy	retro_amel_394,
Callithrix jacchus	ENSCJAG00000002987	1 retrocopy	retro_cjac_4050,
Callithrix jacchus	ENSCJAG00000017156	1 retrocopy	retro_cjac_1087 ,
Cavia porcellus	ENSCPOG00000027003	1 retrocopy	retro_cpor_1102,
Felis catus	ENSFCAG00000005983	1 retrocopy	retro_fcat_790,
Homo sapiens	ENSG00000115350	1 retrocopy	retro_hsap_2765,
Gorilla gorilla	ENSGGOG00000004491	1 retrocopy	retro_ggor_1924,
Mustela putorius furo	ENSMPUG00000008356	1 retrocopy	retro_mputfur_305,
Nomascus leucogenys	ENSNLEG00000001111	1 retrocopy	retro_nleu_670,
Pongo abelii	ENSPPYG00000012258	1 retrocopy	retro_pabe_2246,
Pan troglodytes	ENSPTRG00000012105	1 retrocopy	retro_ptro_1872,