RetrogeneDB ID: retro_cjac_811

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:99448311..99448803(-)
• Located in intron of: ENSCJAG00000020436

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTM1
• Ensembl ID: ENSCJAG00000003123
• Aliases: None
• Description: glutathione S-transferase mu 1 [Source:HGNC Symbol;Acc:4632]

Sequence

>retro_cjac_811
ATGCCTATGATACTGGGATACTGGGACATCCGCGCGCTAGCCCACGCCATCTGCCTGCTCCTGGAATACACACACAGACT
CAAACTACGAGGAAAAGATGTACACAATGGGGGACGCTCCTGACTATGACAGAAGCCAGTGGCTGAATGAAAAGTTCAAG
CTTGGCCTGGACTTTTCCAATCTGCCCTACTTGATTGATGGGGCTCACAAGATCACTCAGAGCCATGCCATCCTGCGCTA
TATTGCCCGCAAGCACAACCTGTGTGGGGAGACAGAAAAGGAGAAGATTTGAGAAGACATTTTGGAGAACCAGCTTATGG
ACAACCACATGCAGCTGGCCAGACTCTGCTACGATCCAGATTTTGAGAGACTAAAGCCAGAATACCTGGAGGGACTTCCT
GAAATGCTGAAGCTCTACTCACAGTTTCTGGGGAAGCGGCCATGGTTTCTTGGGGACAGATCACCTTTGTGGATTTCATC
GCTTATGAAATC

Alignment

ORF - retro_cjac_811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.12 %
• Parental protein coverage: 74.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPMTLGYWDIRGLAHAIRLLLEYT-DSSYEEKK-YTMGDAPDYDRSQWLKEKFKLGLDFPNLPYLIDGAH
          MPM.LGYWDIR.LAHAI.LLLEYT...S..E.K.YTMGDAPDYDRSQWL.EKFKLGLDF.NLPYLIDGAH
Retrocopy MPMILGYWDIRALAHAICLLLEYT>TDSNYEEKMYTMGDAPDYDRSQWLNEKFKLGLDFSNLPYLIDGAH

Parental  KITQSNAILRYIARKHSLCGETEEEKIRVDILENQTMDTRMQLAMLCYNPEFEKLKPKYLEELPEKLKLY
          KITQS.AILRYIARKH.LCGETE.EKI..DILENQ.MD..MQLA.LCY.P.FE.LKP.YLE.LPE.LKLY
Retrocopy KITQSHAILRYIARKHNLCGETEKEKI*EDILENQLMDNHMQLARLCYDPDFERLKPEYLEGLPEMLKLY

Parental  SQFLGKRPWFAGDK-ITFVDFLAYDV
          SQFLGKRPWF.GD..ITFVDF.AY..
Retrocopy SQFLGKRPWFLGDR<ITFVDFIAYEI

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	0.53 RPM	24.03 RPM
SRP051959_heart	0.19 RPM	18.65 RPM
SRP051959_kidney	0.33 RPM	30.02 RPM
SRP051959_liver	0.41 RPM	15.47 RPM
SRP051959_lung	0.29 RPM	19.57 RPM
SRP051959_lymph_node	0.39 RPM	13.36 RPM
SRP051959_skeletal_muscle	0.39 RPM	8.84 RPM
SRP051959_spleen	0.29 RPM	22.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_811 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_811 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_811 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000879	1 retrocopy	retro_cjac_3321,
Callithrix jacchus	ENSCJAG00000003123	7 retrocopies	retro_cjac_1299, retro_cjac_2226, retro_cjac_2463, retro_cjac_2498, retro_cjac_3004, retro_cjac_3084, retro_cjac_811 ,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Gorilla gorilla	ENSGGOG00000005148	2 retrocopies	retro_ggor_1913, retro_ggor_2459,
Nomascus leucogenys	ENSNLEG00000003194	2 retrocopies	retro_nleu_1546, retro_nleu_504,
Pongo abelii	ENSPPYG00000001064	2 retrocopies	retro_pabe_2218, retro_pabe_2990,
Pan troglodytes	ENSPTRG00000001061	2 retrocopies	retro_ptro_1859, retro_ptro_2468,