RetrogeneDB ID: retro_cjac_3888

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285858.1:13839..14627(+)
• 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_3888
TTGCCCACACTAGACATGGCACTGGCCAGCTTGTTGGAGAGGCTGCTACTCATAAACCAGTGCAGGTTTTCTGGACTTAT
AGTTAATGCAGATCTGCTGGATTTGGGTCCAGGGAGTCCCAATGACGGGCTGAGCCTGGCCATGCCCAGCTGGGAGTCTC
AGAAGAGCAGAAAATCAGAATGCTTCATGGAACCACCACCCTGGCCTTCAAGTTCTGCCATGGAGTCATAGTTGCAGCCA
ACTATAGGGCTAAAGTGAGTGCTTACATTGCCTCCACATGGTTAAGAAGGTGACAGAGATCAACCTCTACCTGAAGCCAT
CATGGCTAGGGACACAGTAGATTTTAGCTTCTGAGAATGACTGTTGCTCAGCAATGTCAAATGTATGAGCTTTCAAATAA
GGAATGCATCTCTGTAGCAGCTGTCTCCAAGCTGCTTGCCAACATGTTGTATCAGTACAAAGGCATGGGGCTGTCCATGA
TCTGTGGCTAGGATAAGAGAGGCTCTGGACTCTGCTACATGGACACTGAAGGGAACTGGATCTTGGGGGCCACCTTCTCT
GTAGGTTTTGGCTCTGTGTATGCTTATGGGGTCATGACTCAGGGCTATTCCTATAACCTGGAAATGTAGCAGGCCTATGA
TCTGGCTCACGAAGTGAGCTACCAAGCCACCTGCATAGATGCCTTCTCAGGAGGTGCTGCTAACCTCTACCATGTGCAGG
ATGGCTGGATCCAAGTTTCCAGTGACAATGCAGCTGATCTTCACAACAAGTATGATGGAACTGCCCCA

Alignment

ORF - retro_cjac_3888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.85 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPTLDMALASVLERQLPVNQPGFFGLGGRADLLDLGPGSPSDGLTLAMPGWS-VPEEPGIEMLHGTTTLA
          .PTLDMALAS.LER.L..NQ..F.GL...ADLLDLGPGSP.DGL.LAMP.W..V.EE..I.MLHGTTTLA
Retrocopy LPTLDMALASLLERLLLINQCRFSGLIVNADLLDLGPGSPNDGLSLAMPSWE<VSEEQKIRMLHGTTTLA

Parental  FKFRHGVIVAADSRATAGAYIAS-QTVKKVIEINPYLLGT-MAGGAADCSFWERLL-ARQCRIYELRNKE
          FKF.HGVIVAA..RA...AYIAS...VKKV.EIN.YL....MA....D.SF.E.LL.A.QC..YEL.NKE
Retrocopy FKFCHGVIVAANYRAKVSAYIAS<HMVKKVTEINLYLKPS<MARDTVDFSF*E*LL<AQQCQMYELSNKE

Parental  RISVAAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRG
          .ISVAA.SKLLANM.YQYKGMGLS...MICG.DKRG.GL.Y.D.EGN.I.GATFSVG.GSVYAYGVM..G
Retrocopy CISVAAVSKLLANMLYQYKGMGLS---MICG*DKRGSGLCYMDTEGNWILGATFSVGFGSVYAYGVMTQG

Parental  YSYDLEVEEAYDLARRAIYQATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLHEKYSGSAP
          YSY.LE...AYDLA....YQAT..DA.SGGA.NLYHV..DGWI.VSSDN.ADLH.KY.G.AP
Retrocopy YSYNLEM*QAYDLAHEVSYQATCIDAFSGGAANLYHV-QDGWIQVSSDNAADLHNKYDGTAP

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	20.97 RPM
SRP051959_heart	0.00 RPM	14.56 RPM
SRP051959_kidney	0.00 RPM	16.95 RPM
SRP051959_liver	0.00 RPM	20.77 RPM
SRP051959_lung	0.00 RPM	9.52 RPM
SRP051959_lymph_node	0.00 RPM	5.43 RPM
SRP051959_skeletal_muscle	0.00 RPM	24.55 RPM
SRP051959_spleen	0.00 RPM	10.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3888 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3888 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3888 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,