RetrogeneDB ID: retro_cjac_2110

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:29589905..29590266(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB2
• Ensembl ID: ENSCJAG00000001547
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 2 [Source:HGNC Symbol;Acc:9539]

Sequence

>retro_cjac_2110
CCAAGCTTCACTCAGAGGTGCTGTCTCACTGGTGAGACCAGGAAGCCGGTGAGTGTCGTGCTCTGTCTGACCTGCAGCCC
CTGGCCTCCTGCCACTGTGGAGTACCTCATTGGTATCCAAGGCCCCGACTATGCTCTTGTCACCTCCGACCGGGTGGCCG
CCAGCAATATTGTCCAGATGAAGGACAATCATGACAAGATGTTTAAGATGAGTGAGAAAATATTACTTCTGTGTGTTGGA
AAGGCTGGAAACACACAGTTTGCAGAATATTTTCAGAAAAAAGTGCTACTTTATAAGATGCGAAAATGGGTATGAATCGT
CTCCCACAGCAGCAACTAACTTCACACACGGGAACCTGGCT

Alignment

ORF - retro_cjac_2110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.86 %
• Parental protein coverage: 52.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSFARRCCLTGETGKSARLALCRTWSPWPPATMEYLIGIQGPDYVLVASDRVAASNIVQMKDADHDKMFK
          PSF..RCCLTGET.K.....LC.T.SPWPPAT.EYLIGIQGPDY.LV.SDRVAASNIVQMKD..HDKMFK
Retrocopy PSFTQRCCLTGETRKPVSVVLCLTCSPWPPATVEYLIGIQGPDYALVTSDRVAASNIVQMKD-NHDKMFK

Parental  MSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMR-NGYELSPTAAANFTRRNLA
          MSEKILLLCVG.AG.T.QFAEY.QK.V.LYKMR.NGYE.SPTAA.NFT..NLA
Retrocopy MSEKILLLCVGKAGNT-QFAEYFQKKVLLYKMR>NGYESSPTAATNFTHGNLA

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	0.02 RPM	14.20 RPM
SRP051959_heart	0.02 RPM	10.26 RPM
SRP051959_kidney	0.00 RPM	13.02 RPM
SRP051959_liver	0.00 RPM	18.48 RPM
SRP051959_lung	0.02 RPM	10.74 RPM
SRP051959_lymph_node	0.02 RPM	12.47 RPM
SRP051959_skeletal_muscle	0.00 RPM	18.80 RPM
SRP051959_spleen	0.02 RPM	17.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2110 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2110 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2110 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000715	1 retrocopy	retro_amel_743,
Canis familiaris	ENSCAFG00000003543	1 retrocopy	retro_cfam_1291,
Callithrix jacchus	ENSCJAG00000001547	1 retrocopy	retro_cjac_2110 ,
Dasypus novemcinctus	ENSDNOG00000017663	1 retrocopy	retro_dnov_159,
Equus caballus	ENSECAG00000021615	1 retrocopy	retro_ecab_769,
Echinops telfairi	ENSETEG00000019511	1 retrocopy	retro_etel_1529,
Felis catus	ENSFCAG00000030845	1 retrocopy	retro_fcat_1803,
Macropus eugenii	ENSMEUG00000000421	1 retrocopy	retro_meug_1235,
Monodelphis domestica	ENSMODG00000017902	1 retrocopy	retro_mdom_79,
Mustela putorius furo	ENSMPUG00000014891	1 retrocopy	retro_mputfur_1550,
Ochotona princeps	ENSOPRG00000012259	2 retrocopies	retro_opri_76, retro_opri_762,
Pteropus vampyrus	ENSPVAG00000001871	1 retrocopy	retro_pvam_909,
Sorex araneus	ENSSARG00000000409	2 retrocopies	retro_sara_557, retro_sara_660,
Sarcophilus harrisii	ENSSHAG00000016996	1 retrocopy	retro_shar_794,
Tupaia belangeri	ENSTBEG00000005230	1 retrocopy	retro_tbel_4039,
Tarsius syrichta	ENSTSYG00000005648	2 retrocopies	retro_tsyr_403, retro_tsyr_912,