RetrogeneDB ID: retro_cjac_2910

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:86351815..86352427(+)
• Located in intron of: ENSCJAG00000021570

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD7
• Ensembl ID: ENSCJAG00000015129
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 [Source:HGNC Symbol;Acc:9565]

Sequence

>retro_cjac_2910
GTGGATCATTTCAACCAAATCAGCAAGGTTGGAAATCAAAGTGTACTGTGTGTACTTTTGGGGTCATGGCAGACAAAAGT
ACTTGTATCCAACAGTTCTGGAGTCCCTTTTGATGAAGATGAAAAAGATAATTCCATCTGGTTTTTAGAGCATGATTATT
TGGAAAACATGTATGGAATGTTTCAGAAAATCAGTGCCAGAGAAAGAATAGTTGGGTAGTATCACACAAGCTCTAAACTA
CACAAGAATGACATTGCCATTAAAGAACTCATGAAAAGACACTATCCTACCTCAGTATTGGTATTATTGACATCAAACAA
AGTATCTGGGGCTTCCCACAGAAGCATATATTTCAATGAGAGAAGTCCATGATGATGGAAGTCCAACCTCAAAAACTTTT
GAGCATGCGACTAGTGAAACTGGAGCAGAGGAAGTTGAGGCAGTTGGAGTTGAACACGTGTTATAAGATATCAAAGACAC
TACAGTGGACAGTCTTTGCCAGCTGATCACAAAGAGGTCCATGGTTTGAGGAGACTGAATTCCAACCTTCTGGATATCAG
GAGCTAACTGGAGAAAAGAGCCACAGGCAAGCTGCCCATTAACCACCAGATC

Alignment

ORF - retro_cjac_2910 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 63.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVWFLDHDYLENMYGMFKKVNARE
          VDHFN.I.KVGNQ..V..VLLGSWQ.KVL.VSNS..VPFDED.KD.S.WFL.HDYLENMYGMF.K..ARE
Retrocopy VDHFNQISKVGNQS-VLCVLLGSWQTKVL-VSNSSGVPFDEDEKDNSIWFLEHDYLENMYGMFQKISARE

Parental  RIVGWYHTGPKLHKNDIAINELMKRYCPNSVLV-IIDVK-PKDLGLPTEAYISVEEVHDDGTPTSKTFEH
          RIVG.YHT..KLHKNDIAI.ELMKR..P.SVLV.IID.K..K.LGLPTEAYIS..EVHDDG.PTSKTFEH
Retrocopy RIVG*YHTSSKLHKNDIAIKELMKRHYPTSVLV<IIDIK<TKYLGLPTEAYISMREVHDDGSPTSKTFEH

Parental  VTSEIGAEEAEEVGVEHLLRDIKDTTVGTLSQRIT-NQVHGLKGLNSKLLDIRSYLEKVATGKLPINHQI
          .TSE.GAEE.E.VGVEH.L.DIKDTTV..L.Q.IT...VHGL..LNS.LLDIRS.LEK.ATGKLPINHQI
Retrocopy ATSETGAEEVEAVGVEHVL*DIKDTTVDSLCQLIT<KEVHGLRRLNSNLLDIRS*LEKRATGKLPINHQI

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	0.55 RPM	21.79 RPM
SRP051959_heart	0.40 RPM	23.57 RPM
SRP051959_kidney	0.62 RPM	22.54 RPM
SRP051959_liver	0.11 RPM	22.87 RPM
SRP051959_lung	0.83 RPM	21.99 RPM
SRP051959_lymph_node	0.82 RPM	26.46 RPM
SRP051959_skeletal_muscle	0.13 RPM	40.53 RPM
SRP051959_spleen	0.82 RPM	25.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2910 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2910 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2910 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_372

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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	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Callithrix jacchus	ENSCJAG00000015129	2 retrocopies	retro_cjac_1520, retro_cjac_2910 ,
Homo sapiens	ENSG00000103035	2 retrocopies	retro_hsap_1781, retro_hsap_234,
Gorilla gorilla	ENSGGOG00000009774	1 retrocopy	retro_ggor_2235,
Myotis lucifugus	ENSMLUG00000005416	1 retrocopy	retro_mluc_505,
Macaca mulatta	ENSMMUG00000011125	4 retrocopies	retro_mmul_1242, retro_mmul_372, retro_mmul_417, retro_mmul_566,
Nomascus leucogenys	ENSNLEG00000005608	1 retrocopy	retro_nleu_1310,
Otolemur garnettii	ENSOGAG00000014868	1 retrocopy	retro_ogar_388,
Procavia capensis	ENSPCAG00000014356	1 retrocopy	retro_pcap_399,
Pongo abelii	ENSPPYG00000025918	1 retrocopy	retro_pabe_418,
Pan troglodytes	ENSPTRG00000008343	2 retrocopies	retro_ptro_1192, retro_ptro_205,
Tupaia belangeri	ENSTBEG00000016950	1 retrocopy	retro_tbel_4135,