RetrogeneDB ID: retro_cjac_158

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:130941615..130942623(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022424
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000014400
• Aliases: None
• Description: None

Sequence

>retro_cjac_158
ATGGCGGCGGGCGCGGCTGAGGCGGCTCTAGTGGCCGTGGAGGAGGTCGGCTCAGTCGGGCAGTTTGAGGAGCTGCTGAG
CCTCAAAACCAAGTCCCTCCTTGTGGTCCATTTCTGGGCACCATGGGCTCCACAATGTGCACAGATGAACGAAGTTATGG
CAGAGTTAGCTAAAGAACACCCTCAGGTTTCATTTGCGAAGTTGGAAGCTGAAGGTGTTCCTGAAGTATCTGAAAAATAT
GAAATTAGCTCTGCTCCCACGTTTCTGTTTTTCAAGAATTCTCAGAAAATCGACCGATTAGATGGTGCACATGCTCCAGA
GTTGACCAAAAAAGTTCAGCGACATGCATCTAGTGGCTCCTTCCCACCCAGCGTTAATGAACATCTTAAAGAAGATCTCA
ACCTGCGCTTGAAGAAATTGACTCATGCTGCCCCCTGCATGCTGTTTATGAAAGGAACTCCTCAAGAACCACGCTGTGGT
TTCAGCAAGCAGATGGTGGAAATTCTTCACAAACATAATATTCAGTTTAGCAGTTTTGATATCTTCTCAGATGAAGAGGT
TCGACAGGGGCTCAAAACCTATTCCAACTGGCCTACCTATCCTCAGCTCTATGTTTCTGGAGAGCTCATAGGAGGACTTG
ATATAATTAAGGAGCTAGAAGCATCTGAAGAACTAGATAAAATTTGTCCCAAAGCCCCCAAATTAGAGGAAAGACTCAAA
GTGCTGACAAATAAAGCTTCTGTGATGCTCTTTATGAAAGGAAACAAACAGGAAGCAAAATGTGGATTCAGCAAACAAAT
TCTGGAAATACTAAATAGTACTGGTGTTGAATATGAAACATTCGATATATTGGAGGATGAAGAGGTTCGGCAGGGATTAA
AAGCTTACTCAAATTGGCCAACATACCCTCAGCTGTATGTGAAAGGGGAGCTGGTGGGAGGATTGGATATCGTGAAGGAA
CTGAAAGAAAATGGTGAATTGCTGCCTATACTGAGAGGAGAAAATTAA

Alignment

ORF - retro_cjac_158 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAGAAAAAVGAVEEVGSVGQFEELLSLKAKSLLVVHFWAPWAPQCAQMNEVMAELAKEHPQVSFAKLEA
          MAAGAA.AA..AVEEVGSVGQFEELLSLK.KSLLVVHFWAPWAPQCAQMNEVMAELAKEHPQVSFAKLEA
Retrocopy MAAGAAEAALVAVEEVGSVGQFEELLSLKTKSLLVVHFWAPWAPQCAQMNEVMAELAKEHPQVSFAKLEA

Parental  EGVPEVSEKYEISSVPTFLFFKNSQKIDRLDGAHAPELTKKVQRHASSGSFPPSANEHLKEDLNLRLKKL
          EGVPEVSEKYEISS.PTFLFFKNSQKIDRLDGAHAPELTKKVQRHASSGSFPPS.NEHLKEDLNLRLKKL
Retrocopy EGVPEVSEKYEISSAPTFLFFKNSQKIDRLDGAHAPELTKKVQRHASSGSFPPSVNEHLKEDLNLRLKKL

Parental  TRAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKTYSNWPTYPQLYVSGELV
          T.AAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKTYSNWPTYPQLYVSGEL.
Retrocopy THAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKTYSNWPTYPQLYVSGELI

Parental  GGLDIIKELEASEELDKICPKAPKLEERLKVLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYET
          GGLDIIKELEASEELDKICPKAPKLEERLKVLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYET
Retrocopy GGLDIIKELEASEELDKICPKAPKLEERLKVLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYET

Parental  FDILEDEEVRQGLKAYSNWPTYPQLYVKGELVGGLDIVKELKENGELLPILRGEN
          FDILEDEEVRQGLKAYSNWPTYPQLYVKGELVGGLDIVKELKENGELLPILRGEN
Retrocopy FDILEDEEVRQGLKAYSNWPTYPQLYVKGELVGGLDIVKELKENGELLPILRGEN

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	0.51 RPM	13.78 RPM
SRP051959_heart	0.39 RPM	14.49 RPM
SRP051959_kidney	0.38 RPM	18.48 RPM
SRP051959_liver	0.84 RPM	16.94 RPM
SRP051959_lung	0.52 RPM	15.93 RPM
SRP051959_lymph_node	0.62 RPM	16.57 RPM
SRP051959_skeletal_muscle	0.72 RPM	20.31 RPM
SRP051959_spleen	0.65 RPM	15.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_158 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_158 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_158 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003257	1 retrocopy	retro_amel_1348,
Bos taurus	ENSBTAG00000005027	1 retrocopy	retro_btau_659,
Canis familiaris	ENSCAFG00000013280	1 retrocopy	retro_cfam_285,
Callithrix jacchus	ENSCJAG00000014400	1 retrocopy	retro_cjac_158 ,
Dasypus novemcinctus	ENSDNOG00000010387	1 retrocopy	retro_dnov_2110,
Gorilla gorilla	ENSGGOG00000010771	1 retrocopy	retro_ggor_2308,
Microcebus murinus	ENSMICG00000008544	2 retrocopies	retro_mmur_1394, retro_mmur_89,
Myotis lucifugus	ENSMLUG00000005483	1 retrocopy	retro_mluc_377,
Mus musculus	ENSMUSG00000031068	1 retrocopy	retro_mmus_2480,
Nomascus leucogenys	ENSNLEG00000027088	2 retrocopies	retro_nleu_2322, retro_nleu_249,
Ochotona princeps	ENSOPRG00000017309	1 retrocopy	retro_opri_462,
Pongo abelii	ENSPPYG00000002768	1 retrocopy	retro_pabe_2830,
Pan troglodytes	ENSPTRG00000003060	1 retrocopy	retro_ptro_2320,