RetrogeneDB ID: retro_cjac_2808

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:47141827..47142553(-)
• Located in intron of: ENSCJAG00000007144

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD4
• Ensembl ID: ENSCJAG00000007357
• Aliases: None
• Description: None

Sequence

>retro_cjac_2808
CCAGAGAACAACATGGGCCTTATCACACTGGCTAATGACTGTGAAGTGCTGACCACACTCACCCCAGACACTGGTCGTAT
CCCGTCCAAGCTACACACTGTCCAACCCAAGGGCAAGATCACCTTCTGCACTGGCATCCACGTGGCCCATCTGGCTCTGA
AGCACCGTCAGGGCAAGAATCACAAGATGCGCATCATTGCCTTTGTGGGAAGACCAGTGAAGGACAATAAGAAGGATCTG
GTAAAACTGGCTAAATGACTCAAGAAGGAGAAAGTAAATGTTAACATTATCAATTTTGGGGAAGAGGAGGTGAACACAGA
AAAGCTGACAGCCTTTGTAAACATGCTGAATGGCAAAAATGGAACCAGTTATCATCTGGTGACAGTACCTCCTGGGCCCA
GCTTGGCCGATGCTAGCATCAGTTCTCCGATTTTGCCTGGTGAAGGTAGTGCCATGCTGGGTCTTGGTGCCAGTGACTTT
GAATTTGCAGTAGATCCCAGTGCTGATCCTGAGCTGGCCTTGGCCCTTCATGTATCTATGGAAGAGCAGTGGCAGCGGCA
GGAGGAGGAGGCCTGGCGGGCAGCTGCAGCTTCTGCTGCTAAGGCTGGGACTGCTACGACTGGGACTGAAGACTCAGACG
ATGCCCTGCTGAAGATGACCATCAGCCATCAAGAGTTTGGCCACACTGGGCTCCCTGACCTAAGCAGTATGACTGAGGAA
GAGCAG

Alignment

ORF - retro_cjac_2808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.49 %
• Parental protein coverage: 64.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PENNVGLITLANDCEVLTTLTPDTGRILSKLHTVQPKGKITFCTGIRVAHLALKHRQGKNHKMRIIAFVG
          PENN.GLITLANDCEVLTTLTPDTGRI.SKLHTVQPKGKITFCTGI.VAHLALKHRQGKNHKMRIIAFVG
Retrocopy PENNMGLITLANDCEVLTTLTPDTGRIPSKLHTVQPKGKITFCTGIHVAHLALKHRQGKNHKMRIIAFVG

Parental  SPVEDNEKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLADALI
          .PV.DN.KDLVKLAK.LKKEKVNV.IINFGEEEVNTEKLTAFVN.LNGK.GT..HLVTVPPGPSLADA.I
Retrocopy RPVKDNKKDLVKLAK*LKKEKVNVNIINFGEEEVNTEKLTAFVNMLNGKNGTSYHLVTVPPGPSLADASI

Parental  SSPILAGEGGAMLGLGASDFEFGVDPSADPELALALRVSMEEQRQRQEEEARRAAAASAAEAGIATTGTE
          SSPIL.GEG.AMLGLGASDFEF.VDPSADPELALAL.VSMEEQ.QRQEEEA.R...A.AA..........
Retrocopy SSPILPGEGSAMLGLGASDFEFAVDPSADPELALALHVSMEEQWQRQEEEAWR---AAAASXXXXXXXXX

Parental  GERDSDDALLKMTISQQEFGRTGLPDLSSMTEEEQ
          ...DSDDALLKMTIS.QEFG.TGLPDLSSMTEEEQ
Retrocopy XXXDSDDALLKMTISHQEFGHTGLPDLSSMTEEEQ

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	0.16 RPM	17.31 RPM
SRP051959_heart	0.32 RPM	28.61 RPM
SRP051959_kidney	0.18 RPM	29.26 RPM
SRP051959_liver	0.24 RPM	33.36 RPM
SRP051959_lung	0.20 RPM	23.67 RPM
SRP051959_lymph_node	0.55 RPM	21.48 RPM
SRP051959_skeletal_muscle	0.15 RPM	76.41 RPM
SRP051959_spleen	0.25 RPM	24.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2808 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2808 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2808 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012565	1 retrocopy	retro_cfam_591,
Callithrix jacchus	ENSCJAG00000007357	1 retrocopy	retro_cjac_2808 ,
Dasypus novemcinctus	ENSDNOG00000007446	1 retrocopy	retro_dnov_1556,
Homo sapiens	ENSG00000159352	1 retrocopy	retro_hsap_2531,
Nomascus leucogenys	ENSNLEG00000010139	1 retrocopy	retro_nleu_1450,
Pongo abelii	ENSPPYG00000000871	1 retrocopy	retro_pabe_1862,
Pan troglodytes	ENSPTRG00000013893	1 retrocopy	retro_ptro_1474,
Sus scrofa	ENSSSCG00000006628	1 retrocopy	retro_sscr_981,
Tupaia belangeri	ENSTBEG00000016911	1 retrocopy	retro_tbel_238,
Tursiops truncatus	ENSTTRG00000007019	1 retrocopy	retro_ttru_903,