RetrogeneDB ID: retro_cjac_2903

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:80585456..80585756(+)
• Located in intron of: ENSCJAG00000013788

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000010668
• Aliases: None
• Description: None

Sequence

>retro_cjac_2903
GATGGGTTCCTCTCCGAACTCACCCAGCAGCTGGCGCAGGCCACTGGCAAGTCACCCCAGTACATTGAGGTGCACTTGGT
CCCGGATCAGCTCGAGGCCTTGTGCTGCTCCTGCAAGCAGTGCGCGCTCTGCAGCCTGCACAGCATCTGCAAGCTTAGCG
GCCCGCAGAACTGCTCTTACACGAAGCTACTGTGCTGCCTGTGGGCCGAGCGCCTGTGCATCAGCCAAGACAGAGTCTAT
ATCAACTATAACATAAACGCGGCCAACCTTTTAACTTCAGGCTGGAACAACTATACCTTC

Alignment

ORF - retro_cjac_2903 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.29 %
• Parental protein coverage: 85.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DGFLSELTQQLAQATGKPPQYIAVHVVPDQLMAFGGSSDPCALCSLHSIGKIGGAQNRSYSKLLCGLLAE
          DGFLSELTQQLAQATGK.PQYI.VH.VPDQL.A...S...CALCSLHSI.K..G.QN.SY.KLLC.L.AE
Retrocopy DGFLSELTQQLAQATGKSPQYIEVHLVPDQLEALCCSCKQCALCSLHSICKLSGPQNCSYTKLLCCLWAE

Parental  RLRISPDRVYINYYDMNASNV---GWNNSTF
          RL.IS.DRVYIN.Y..NA.N....GWNN.TF
Retrocopy RLCISQDRVYIN-YNINAANLLTSGWNNYTF

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	0.07 RPM	3.73 RPM
SRP051959_heart	0.05 RPM	5.14 RPM
SRP051959_kidney	0.02 RPM	6.52 RPM
SRP051959_liver	0.00 RPM	2.97 RPM
SRP051959_lung	0.07 RPM	4.46 RPM
SRP051959_lymph_node	0.14 RPM	4.75 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.01 RPM
SRP051959_spleen	0.06 RPM	3.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2903 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2903 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2903 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010668	3 retrocopies	retro_cjac_2903 , retro_cjac_3132, retro_cjac_357,
Cavia porcellus	ENSCPOG00000013520	1 retrocopy	retro_cpor_879,
Dasypus novemcinctus	ENSDNOG00000014555	1 retrocopy	retro_dnov_36,
Equus caballus	ENSECAG00000012792	1 retrocopy	retro_ecab_1122,
Echinops telfairi	ENSETEG00000012052	3 retrocopies	retro_etel_2001, retro_etel_2046, retro_etel_509,
Mus musculus	ENSMUSG00000033307	8 retrocopies	retro_mmus_1573, retro_mmus_1759, retro_mmus_1878, retro_mmus_2182, retro_mmus_2444, retro_mmus_3016, retro_mmus_3315, retro_mmus_489,
Ochotona princeps	ENSOPRG00000012184	1 retrocopy	retro_opri_968,
Rattus norvegicus	ENSRNOG00000006589	6 retrocopies	retro_rnor_137, retro_rnor_1608, retro_rnor_1644, retro_rnor_2263, retro_rnor_31, retro_rnor_361,