RetrogeneDB ID: retro_cjac_450

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:95666787..95667138(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC4
• Ensembl ID: ENSCJAG00000013703
• Aliases: None
• Description: trafficking protein particle complex 4 [Source:HGNC Symbol;Acc:19943]

Sequence

>retro_cjac_450
CTCACTTCTAAAGAGAAGCTCATGCTGGCTTCCATGTTCCACTCCCCCTTTGCCATTGGCTCCCAGCTGTCTCCTGAGTA
GGGAAGCTCAGGCATTAATATGCTGGAGAAAGACACATTCAAAATGCACTGCCAGCAGACACTGATAGGGATCAAGTTTG
TGGTTCTAGCAGATCATAGGCAAGCTGGAAGAGATTCTCTTCTCCAAAAGATTTATGAGATTTACTCAGACTCTGCCCTC
AGGAATCCATTCTACTCCTTAGAAATGCCCATCGGGTGTGAGCTATTTGACCAGAATCTGAAGCTAGGCCTGGAAGTGGC
AGAGAAGGCTGGAACTTTTGGACCTGGGTCA

Alignment

ORF - retro_cjac_450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.18 %
• Parental protein coverage: 53.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTSNEKLMLASMFHSLFAIGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLADPRQAGIDSLLRK
          LTS.EKLMLASMFHS.FAIGSQLSPE.GSSGI.MLE.DTFK.HC.QTL.GIKFVVLAD.RQAG.DSLL.K
Retrocopy LTSKEKLMLASMFHSPFAIGSQLSPE*GSSGINMLEKDTFKMHCQQTLIGIKFVVLADHRQAGRDSLLQK

Parental  IYEIYSDFALKNPFYSLEMPIRCELFDQNLKLALEVAEKAGTFGPGS
          IYEIYSD.AL.NPFYSLEMPI.CELFDQNLKL.LEVAEKAGTFGPGS
Retrocopy IYEIYSDSALRNPFYSLEMPIGCELFDQNLKLGLEVAEKAGTFGPGS

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	5.46 RPM
SRP051959_heart	0.00 RPM	5.05 RPM
SRP051959_kidney	0.00 RPM	14.38 RPM
SRP051959_liver	0.00 RPM	18.30 RPM
SRP051959_lung	0.00 RPM	8.48 RPM
SRP051959_lymph_node	0.00 RPM	9.06 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.78 RPM
SRP051959_spleen	0.00 RPM	9.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_450 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_450 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_450 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012383	1 retrocopy	retro_cfam_760,
Callithrix jacchus	ENSCJAG00000013703	1 retrocopy	retro_cjac_450 ,
Dasypus novemcinctus	ENSDNOG00000007885	1 retrocopy	retro_dnov_46,
Myotis lucifugus	ENSMLUG00000004759	1 retrocopy	retro_mluc_1438,
Ictidomys tridecemlineatus	ENSSTOG00000014340	1 retrocopy	retro_itri_1252,