RetrogeneDB ID: retro_cjac_4076

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:65646883..65647522(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB5
• Ensembl ID: ENSCJAG00000008299
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 5 [Source:HGNC Symbol;Acc:9542]

Sequence

>retro_cjac_4076
CCCACACTAGACATGGCACCCGCCCGTGTGTTGGAGAGACCAGTATACGTGAACCAGTGTGGGTTTTTCAGACTCGAAGG
TTGTGCAGATCTGCTGAATCTGGGTCCAGGGTGTCCCAGTGATAGGCTGATCCTGGCTGTGACTGGCTGGGGTGTCCCAG
AGGAGCCAGGAATCGAAATGCTTCATGGAACAACCGCCTTGGCCTTCAGGTTCCACCATGGAGTCATAGTGCTGTCAACT
CCAGAGCGACAGCACGTGCTTACATTGCCTCCCAGATGGTGAACAAGATTATAGAGATAAATCCCTCCCTACTAGGCACC
ATGGCTGAGGACTTAGTGGATTGTAGCTTCTGGGAATAGCTGTTGGCTGAGCAATGTTGAATCTATGAGCTTCGACATAA
GGAATGCATCTCTGTACAGCTGCCTCAAAGCAGCTTGCCAACATGGTGTATCAGTACAAAGGCATGGGGCTGTCCATGGG
CAACATGATCTGTGGCTGGGATAAGAGAAGACCTTGCCTCTACTATGTGGACAGTGAAGGGAACTGGATCTCAGGGGCCA
CCCTCTCTGTAGGTTCTTGCTCTGTATATGTGAATGGGTCATGGATCAGGGTTATTCCTATGACCTGGAAGTGGCGCAG

Alignment

ORF - retro_cjac_4076 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.5 %
• Parental protein coverage: 79.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PTLDMALASVLERQLPVNQPGFFGLGGRADLLDLGPGSPSDGLTLAMPGWSVPEEPGIEMLHGTTTLAFK
          PTLDMA.A.VLER...VNQ.GFF.L.G.ADLL.LGPG.PSD.L.LA..GW.VPEEPGIEMLHGTT.LAF.
Retrocopy PTLDMAPARVLERPVYVNQCGFFRLEGCADLLNLGPGCPSDRLILAVTGWGVPEEPGIEMLHGTTALAFR

Parental  FRHGVIV-AADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISV
          F.HGVIV.A..SRATA.AYIASQ.V.K.IEINP.LLGTMA....DCSFWE.LLA.QC.IYELR.KE.ISV
Retrocopy FHHGVIV<AVNSRATARAYIASQMVNKIIEINPSLLGTMAEDLVDCSFWE*LLAEQC*IYELRHKECISV

Parental  -AAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYG-VMDRGYS
          ..AASK.LANMVYQYKGMGLSMG.MICGWDKR.P.LYYVDSEGN.ISGAT.SVGS.SVY..G.VMD.GYS
Retrocopy <TAASKQLANMVYQYKGMGLSMGNMICGWDKRRPCLYYVDSEGNWISGATLSVGSCSVYVNG<VMDQGYS

Parental  YDLEVEE
          YDLEV..
Retrocopy YDLEVAQ

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	0.47 RPM	20.97 RPM
SRP051959_heart	1.49 RPM	14.56 RPM
SRP051959_kidney	0.75 RPM	16.95 RPM
SRP051959_liver	0.32 RPM	20.77 RPM
SRP051959_lung	0.94 RPM	9.52 RPM
SRP051959_lymph_node	0.71 RPM	5.43 RPM
SRP051959_skeletal_muscle	0.24 RPM	24.55 RPM
SRP051959_spleen	0.84 RPM	10.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4076 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4076 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4076 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008299	4 retrocopies	retro_cjac_1983, retro_cjac_35, retro_cjac_3888, retro_cjac_4076 ,
Homo sapiens	ENSG00000100804	2 retrocopies	retro_hsap_1634, retro_hsap_95,
Gorilla gorilla	ENSGGOG00000026856	2 retrocopies	retro_ggor_1232, retro_ggor_156,
Latimeria chalumnae	ENSLACG00000015194	1 retrocopy	retro_lcha_3,
Macropus eugenii	ENSMEUG00000003572	1 retrocopy	retro_meug_28,
Myotis lucifugus	ENSMLUG00000014281	1 retrocopy	retro_mluc_1428,
Macaca mulatta	ENSMMUG00000006007	1 retrocopy	retro_mmul_1558,
Mus musculus	ENSMUSG00000022193	1 retrocopy	retro_mmus_2887,
Nomascus leucogenys	ENSNLEG00000014891	2 retrocopies	retro_nleu_1063, retro_nleu_2936,
Oryctolagus cuniculus	ENSOCUG00000013109	1 retrocopy	retro_ocun_176,
Pongo abelii	ENSPPYG00000005654	1 retrocopy	retro_pabe_171,
Sus scrofa	ENSSSCG00000002036	1 retrocopy	retro_sscr_616,