RetrogeneDB ID: retro_cjac_2783

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:3378142..3378496(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000034823
• Aliases: None
• Description: Glutathione S-transferase [Source:UniProtKB/TrEMBL;Acc:F7HBV1]

Sequence

>retro_cjac_2783
CTGCTGGAGACAGCTGGAGTGCAGTTGGAGAAGAATTTCTTGAAACAGGAGAACAATACAGAACGTCACGGAAGGACGAA
CACCTGCTGTTTGGTCACGTGCCTTTGGTTGAAATTGGTGGAATCATGCTGACACAGATGAGAGCCGTCCTCAGCTGCCT
TGCTGCCAACTCCACTTTTCCGTGGGAAGGGCCTGAAGGACAGAATCGGGAATGGTTGCAGGTGGACGGCACCCTGATGG
GGAAGACGCTGGCTGCATTCTGACTCCCTCAGGAAAAAGGAGAAACTTGTGTCAGTCGTGAGGAGAGACAAAACCCAGGA
CTTGCCCATATTTGAAAAGCTTTTGAAAGGACAC

Alignment

ORF - retro_cjac_2783 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.54 %
• Parental protein coverage: 54.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LLAAAGVEFE-EEFLETREQYEKLQKDGCLLFGQVPLVEVDGMMLTQTRAILSYLAAKFN-FYGKDLKER
          LL..AGV..E.EEFLET.EQY....KD..LLFG.VPLVE..G.MLTQ.RA.LS.LAA....F.GK.LK.R
Retrocopy LLETAGVQLE<EEFLETGEQYRTSRKDEHLLFGHVPLVEIGGIMLTQMRAVLSCLAANST>FRGKGLKDR

Parental  V-RIDMYVDGTLDLMAMIMLAPFQRPEEKQETLASVIQK-AKARYFP-VFEKILKDH
          ..R....VDGT..LM.....A.F..P.EK.ET..S......K.R..P..FEK.LK.H
Retrocopy I<REWLQVDGT--LMGKTLAA-F*LPQEKGETCVSREER<TKPRTCP<IFEKLLKGH

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	0.07 RPM
SRP051959_heart	0.05 RPM	0.07 RPM
SRP051959_kidney	0.04 RPM	0.16 RPM
SRP051959_liver	0.35 RPM	1.28 RPM
SRP051959_lung	0.00 RPM	0.37 RPM
SRP051959_lymph_node	0.05 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.02 RPM	0.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2783 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2783 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2783 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011287	1 retrocopy	retro_cjac_4055,
Callithrix jacchus	ENSCJAG00000034823	2 retrocopies	retro_cjac_2783 , retro_cjac_2841,
Otolemur garnettii	ENSOGAG00000031992	1 retrocopy	retro_ogar_2737,
Rattus norvegicus	ENSRNOG00000030449	1 retrocopy	retro_rnor_165,