RetrogeneDB ID: retro_cjac_3221

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:57798920..57799802(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC6
• Ensembl ID: ENSCJAG00000007126
• Aliases: None
• Description: None

Sequence

>retro_cjac_3221
ATTGAAAGAAGGAAGCAGCTTCTCTTCATGGTAGACCCTAGAGATAAGGCACTTCAGGACTACCCAAGAAGCTGCTTGAG
CACAGGGAGATCGACAGCCGTCTTAAGGAGTTAAGGAAACAATTAAAAGAACTTACAAGCAGTATGAAAAGTCTGAAAAT
GATCTGAAAGTCCTACCAAGTGTTGGGCAGACTGTGGGTGAAGTGCTTAAACAGTTAACTGAAGAAAAATTCATTGTTAA
AGCTACAAATGGACCAAGAAATGTTGTGGGTTGTCGTCAACAGCTTGACAAAAGTAAGCTGAAGCCAGGAATAAGAGTTG
CTTTGGAGATGACAACACGAACTCTCATGAGATATTTGCCAAGAGAGGTGGATCCACTGATTCATGATATGTCTCATGAG
GACCCTGGGAATGTTTCTTATTCTGAGATTGGAGGGCTAGCGAAACAGATCCGGGAATTAAGAGAGGTAAATTACCTCTT
CCATACCCAGTTATTTCAGCATATAGGAATAATACCTCCAAAAGGCTGTTTGTTTACAGACCACCAGGTACGGTAAAAAC
ACTCTTGGCACAAGCCATTGCTAGCCGGCTGGACTGCAATTTCTTAAAGGCTGTATCTAGTTTTATTGTAGACAAGTACA
TTGGTGAAAGTGCTCGTTTGATCAGAGAAATGTTTAATTATGCCAGGGACCGTCAACCATGAATCATTTTTATAGATGAA
ATGGATGGTATTGGTGGTCGTTGGTTTTCTGAGGGTACTTCAGCTGACAGAGAGTGTCACAGAACTTTAATGGAGTTACT
GAATCAAATGGATGGAGTTGATACTCTGCATAGAGTTAAAATGGTCGTGGCTACAAACAGACCAAATACACTAGATCCTG
CT

Alignment

ORF - retro_cjac_3221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.67 %
• Parental protein coverage: 73.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IPYERRLLIMADPRDKALQDYR-KKLLEHKEIDGRLKELREQLKELT-KQYEKSENDLKALQSVGQIVGE
          I.....LL.M.DPRDKALQDY..KKLLEH.EID.RLKELR.QLKELT.KQYEKSENDLK.L.SVGQ.VGE
Retrocopy IERRKQLLFMVDPRDKALQDYP<KKLLEHREIDSRLKELRKQLKELT<KQYEKSENDLKVLPSVGQTVGE

Parental  VLKQLTEEKFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVYNMSHEDPGN
          VLKQLTEEKFIVKATNGPR.VVGCR.QLDKSKLKPG.RVAL.MTT.T.MRYLPREVDPL...MSHEDPGN
Retrocopy VLKQLTEEKFIVKATNGPRNVVGCRQQLDKSKLKPGIRVALEMTTRTLMRYLPREVDPLIHDMSHEDPGN

Parental  VSYSEIGGLSEQIRELREVIELPLTNPELFQRVGIIPPKGCL-LYGPPGTGKTLLARAVASQLDCNFLKV
          VSYSEIGGL..QIRELREV....L....LFQ..GIIPPKGCL..Y.PPGT.KTLLA.A.AS.LDCNFLK.
Retrocopy VSYSEIGGLAKQIRELREVNY--LFHTQLFQHIGIIPPKGCL<VYRPPGTVKTLLAQAIASRLDCNFLKA

Parental  VSSSIVDKYIGESARLIREMFNYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFD
          VSS.IVDKYIGESARLIREMFNYARD.QP.IIF.DE.D.IGGR.FSEGTSADRE..RTLMELLNQMDG.D
Retrocopy VSSFIVDKYIGESARLIREMFNYARDRQP*IIFIDEMDGIGGRWFSEGTSADRECHRTLMELLNQMDGVD

Parental  TLHRVKMIMATNRPDTLDPA
          TLHRVKM..ATNRP.TLDPA
Retrocopy TLHRVKMVVATNRPNTLDPA

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	32.04 RPM
SRP051959_heart	0.00 RPM	33.41 RPM
SRP051959_kidney	0.02 RPM	35.41 RPM
SRP051959_liver	0.00 RPM	34.66 RPM
SRP051959_lung	0.00 RPM	27.13 RPM
SRP051959_lymph_node	0.00 RPM	29.79 RPM
SRP051959_skeletal_muscle	0.00 RPM	44.18 RPM
SRP051959_spleen	0.02 RPM	29.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3221 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3221 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3221 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007126	2 retrocopies	retro_cjac_204, retro_cjac_3221 ,
Cavia porcellus	ENSCPOG00000009477	1 retrocopy	retro_cpor_47,
Homo sapiens	ENSG00000100519	2 retrocopies	retro_hsap_1022, retro_hsap_4059,
Gorilla gorilla	ENSGGOG00000002152	2 retrocopies	retro_ggor_2727, retro_ggor_808,
Macropus eugenii	ENSMEUG00000007084	3 retrocopies	retro_meug_1700, retro_meug_2090, retro_meug_923,
Monodelphis domestica	ENSMODG00000014500	1 retrocopy	retro_mdom_438,
Nomascus leucogenys	ENSNLEG00000012518	2 retrocopies	retro_nleu_559, retro_nleu_900,
Otolemur garnettii	ENSOGAG00000010011	1 retrocopy	retro_ogar_3101,
Pongo abelii	ENSPPYG00000005820	2 retrocopies	retro_pabe_3334, retro_pabe_858,
Pan troglodytes	ENSPTRG00000006352	2 retrocopies	retro_ptro_2752, retro_ptro_699,
Rattus norvegicus	ENSRNOG00000007203	1 retrocopy	retro_rnor_1480,
Tursiops truncatus	ENSTTRG00000003880	1 retrocopy	retro_ttru_117,