RetrogeneDB ID: retro_cjac_35

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:47116308..47117211(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023221
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_35
ATGGCTCTGCAGGATGTGTGCAAGTGGCAGGCCCCTGACACCCAGGGACCATCACCTTACCTGCCTCAGGCCGGCGGCTG
GCTTGTGCCCCGAGGCTGTGACCCTCAAACCTTCCTGCAGATCCATGGCCCCAGACTGGCCCATGGCACCACCACCCTGG
CCTTCCGCTTCCGTCATGGAGTCATCGCTGCAGCCGACACACGTTCCTCCTGTGGCAGCTACGTGGCGTGTCTGGCCTCA
TGCAAGGTCATCCCTGTGCACCAGCACCTCCTGGGTACCACCTCTGGCACCTCCGCTGACTGTGCCACCTGGTATCGGGT
GCTACAGCGGGAGCTGCGGCTTCGGGAACTGAGGGAGGGTCAGCTGCCCAGTGTGGCCAGTGCTGCCAAGCTCTTGTCAG
CCATGATGTCTCGCTACCGGGGACTGGATCTCTGTGTGGCCACTGCCCTGTGTGGCTGGGACCGCTCTGGCCCTACTCTC
TTCTACGTCTATAGCGACGGCACCCGCCTGCAGGGGGACATCTTCTCTGTGGGCTCTGGATCTCCCTATGCCTACGGCGT
GCTAGACCGCGGCTATCACTACGACATGACCAACCAGGAAGCCTATGCCCTGGCTCGCTGCGCGGTGGCCCACGCCACCC
ACCGCGATGCCTATTCAGGGGGCTCTGTAGACCTTTTCCATGTTCGGGAGAGTGGATGGGAGCATGTGTCACGCAGTGAT
GCCTGTGTGCTGTACGTGGAGCTGCAGAAGCTCCTGGAGCCAGAGCCAGAGGAGGAGGCCAGCCACGCCCATCCTGAGCC
TGCCACTGCCCACAGAGCTGCAGAAGATAGAGAGCTCTCTATGAGGCCAGGGAAGATGATGCCAGGAGACTCCAGGATGC
CAGCAGGGACTGAGACACTGTGA

Alignment

ORF - retro_cjac_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.68 %
• Parental protein coverage: 75.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GIEMLHGTTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQC
          G....HGTTTLAF.FRHGVI.AAD.R...G.Y.A.....KVI.....LLGT..G..ADC..W.R.L.R..
Retrocopy GPRLAHGTTTLAFRFRHGVIAAADTRSSCGSYVACLASCKVIPVHQHLLGTTSGTSADCATWYRVLQREL

Parental  RIYELRNKERISVAAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSV
          R..ELR.....SVA.A.KLL..M...Y.G..L...T..CGWD..GP.L.YV.S.G.R..G..FSVGSGS.
Retrocopy RLRELREGQLPSVASAAKLLSAMMSRYRGLDLCVATALCGWDRSGPTLFYVYSDGTRLQGDIFSVGSGSP

Parental  YAYGVMDRGYSYDLEVEEAYDLARRAIYQATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLH
          YAYGV.DRGY.YD....EAY.LAR.A...AT.RDAYSGG.V.L.HVRE.GW..VS......L.
Retrocopy YAYGVLDRGYHYDMTNQEAYALARCAVAHATHRDAYSGGSVDLFHVRESGWEHVSRSDACVLY

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	0.02 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	0.02 RPM	10.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_35 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_35 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_35 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_95
Pan troglodytes	retro_ptro_97
Gorilla gorilla	retro_ggor_156
Pongo abelii	retro_pabe_171
Oryctolagus cuniculus	retro_ocun_176
Bos taurus	retro_btau_11
Sus scrofa	retro_sscr_90
Canis familiaris	retro_cfam_75
Equus caballus	retro_ecab_18

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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,