RetrogeneDB ID: retro_cjac_2852

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:132972032..132972604(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB3
• Ensembl ID: ENSCJAG00000008246
• Aliases: None
• Description: Proteasome subunit beta type [Source:UniProtKB/TrEMBL;Acc:F7GPT9]

Sequence

>retro_cjac_2852
TCTATTATGTCCTGTAATGGAGGAGCCATCATGGCCATGTAGGGGAAGGACTGTGTGGCCATTGCTGCAGACAGGCACTT
TGGGATCCAGGCCCGGATGGTGACCACAGGCTTCCAGATCTTTCCCACTGGTGATCGGCCGTACATCGGTCTGGCTGGGC
TCGCTACTGATGTCCAGACAGTTGCCCAGTGCCTCAAGTTCTACCTGAACCTGTATTCGCTGAAGGAAGATCAGTAGATC
AAATCTTGTACCCTCATGAGCCTGGTGGCCAATCTCTTGTATGAGAAACGTCTTGGCCCCTCCTACACTGAGCCAGTCAT
TGCTGGGTTGGACCCAAAGACCTGGAAGCCCTTCAGTTGCCTCTAGACCTCATTGGCTGCCCCATGGTGACTGCTGATTT
TGTGGTCAGTGGCACCTATGCCAAACAAATGTATAGAATTTGTGAGTCCCTCTGGGAGCCCAATATGGATCCAGAACACC
TGTTTGAAACCATCTCCCATGCCATGCTCAATGCTGTGGACTGGGATGCAGTGTCAGGCATGGGAGTCATTGTCCACATC
ACCGAGGACAAA

Alignment

ORF - retro_cjac_2852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.65 %
• Parental protein coverage: 94.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRL
          SIMS.NGGA.MAM.GK.CVAIAADR.FGIQA.MVTT.FQ.IFP.GDR.YIGLAGLATDVQTVAQ.LKF.L
Retrocopy SIMSCNGGAIMAM*GKDCVAIAADRHFGIQARMVTTGFQ-IFPTGDRPYIGLAGLATDVQTVAQCLKFYL

Parental  NLYELKEGRQIKPYTLMSMVANLLYEKRVWPYYTEPVIAGWDPKL-KPFIC-SLNLIGCPMGTDDYVVSG
          NLY.LKE...IK..TLMS.VANLLYEKR..P.YTEPVIAG.DPK..KPF.C..L.LIGCPM.T.D.VVSG
Retrocopy NLYSLKEDQ*IKSCTLMSLVANLLYEKRLGPSYTEPVIAGLDPKTWKPFSC<PLDLIGCPMVTADFVVSG

Parental  TWC-TMYGMCQSLWEATLDPEHLFETISQAMLNAVDRDAVSGMGVIVHIIENQ
          T....MY..C.SLWE...DPEHLFETIS.AMLNAVD.DAVSGMGVIVHI.E..
Retrocopy TYAKQMYRICESLWEPNMDPEHLFETISHAMLNAVDWDAVSGMGVIVHITEDK

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	0.18 RPM	11.85 RPM
SRP051959_heart	0.11 RPM	10.61 RPM
SRP051959_kidney	0.13 RPM	13.60 RPM
SRP051959_liver	0.15 RPM	15.01 RPM
SRP051959_lung	0.02 RPM	7.73 RPM
SRP051959_lymph_node	0.00 RPM	10.02 RPM
SRP051959_skeletal_muscle	0.26 RPM	14.24 RPM
SRP051959_spleen	0.08 RPM	9.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2852 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2852 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2852 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2387
Gorilla gorilla	retro_ggor_103
Pongo abelii	retro_pabe_2153

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016587	2 retrocopies	retro_cfam_135, retro_cfam_532,
Callithrix jacchus	ENSCJAG00000008246	1 retrocopy	retro_cjac_2852 ,
Equus caballus	ENSECAG00000000987	1 retrocopy	retro_ecab_476,
Erinaceus europaeus	ENSEEUG00000015275	1 retrocopy	retro_eeur_10,
Homo sapiens	ENSG00000108294	2 retrocopies	retro_hsap_1121, retro_hsap_2387,
Gorilla gorilla	ENSGGOG00000007067	2 retrocopies	retro_ggor_103, retro_ggor_876,
Loxodonta africana	ENSLAFG00000002233	1 retrocopy	retro_lafr_70,
Macropus eugenii	ENSMEUG00000004131	2 retrocopies	retro_meug_1804, retro_meug_551,
Microcebus murinus	ENSMICG00000002997	1 retrocopy	retro_mmur_397,
Macaca mulatta	ENSMMUG00000012363	1 retrocopy	retro_mmul_868,
Monodelphis domestica	ENSMODG00000012614	2 retrocopies	retro_mdom_1722, retro_mdom_1812,
Mus musculus	ENSMUSG00000069744	8 retrocopies	retro_mmus_1449, retro_mmus_1551, retro_mmus_1790, retro_mmus_1938, retro_mmus_2110, retro_mmus_41, retro_mmus_46, retro_mmus_536,
Nomascus leucogenys	ENSNLEG00000000594	3 retrocopies	retro_nleu_1511, retro_nleu_188, retro_nleu_371,
Oryctolagus cuniculus	ENSOCUG00000002598	1 retrocopy	retro_ocun_561,
Pongo abelii	ENSPPYG00000008505	2 retrocopies	retro_pabe_2153, retro_pabe_927,
Pteropus vampyrus	ENSPVAG00000002270	1 retrocopy	retro_pvam_822,
Rattus norvegicus	ENSRNOG00000012938	7 retrocopies	retro_rnor_1016, retro_rnor_2094, retro_rnor_2448, retro_rnor_2537, retro_rnor_2804, retro_rnor_743, retro_rnor_8,
Ictidomys tridecemlineatus	ENSSTOG00000014258	3 retrocopies	retro_itri_527, retro_itri_935, retro_itri_936,