RetrogeneDB ID: retro_cjac_3122

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:29487856..29488650(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UFSP2
• Ensembl ID: ENSCJAG00000005943
• Aliases: None
• Description: None

Sequence

>retro_cjac_3122
AAAAAAATTCTTATAACCATTTCATATCCTTCAGGAATACCAGATGGTCAGCTGCAGGCTTATAGAAAGGAGTTACATGA
TCTCTTCAGTCTGTCTCATGACAGATCCTATTTCAAAAGGTCTAATGCTTATCACTTTCCAGATGAGCCGCCATACAAAG
ATGGTTACAGTAGAAATCCACATATTTATCTCCATCTACCTAACATGGAGACTGGTATGATTTATGTGGTCCAGGACATA
TATGTTTATCATCATTATATGCAGGACTGGATAGGTGACAATGGCTGGGGCTGTGCTTAATGATTTCTGCAGATTATCTG
CTCTTGGTTCAAACATCAGGAATACACAGAGAAGTCCATTCCAACACACAGAGAAATTCAGCAGGCTCTAGTTGATGCTG
GTGACAAACCAGCAACATTTGTTGGATCACTGCAGTAGATTGGATCTATTGAGGTACAGCTGGTACTAAGCCAATTGACT
GGTATAAATTAAAAAATACTGTTTGTCAGCCAAGGTTCAGAAATGGCCTCTCAAGGACAGGAACTGGCTAATCATTTCCA
AAGCGAAGAGACTTCAGTTATAATCGGGGAGGAGTTTTGGCCCAAACAATACTAGGAGTTGCATGGGATAAGACTATAGG
CCAGATAAAGTTTCTGATTCTAGATCCACATTATACAGGTGCTGAAAACCTGCAAGTTATTTTGGAAAAGGGCTGATGTG
GAGGAAAGGGCCCAGACTTTTGGAACAAGTATGCTTACGATAACTTATGTCTTCCTCAGTGACCAAATATGATT

Alignment

ORF - retro_cjac_3122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.04 %
• Parental protein coverage: 57.3 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKSLVTISYPSGIPDGQLQAYRKELHDLFNLPHDRPYFKRSNAYHFPDEP-YKDGYIRNPHAYLNPPNME
          KK.L.TISYPSGIPDGQLQAYRKELHDLF.L.HDR.YFKRSNAYHFPDEP.YKDGY.RNPH.YL..PNME
Retrocopy KKILITISYPSGIPDGQLQAYRKELHDLFSLSHDRSYFKRSNAYHFPDEPPYKDGYSRNPHIYLHLPNME

Parental  TGMVCVAQGIYSYHHYMQDRIDDSGWGCAYRSLQTICSWFKHQGYTERSIPTHREIQQHTKALVDAGDKP
          TGM..V.Q.IY.YHHYMQD.I.D.GWGCA...LQ.ICSWFKHQ.YTE.SIPTHREIQQ...ALVDAGDKP
Retrocopy TGMIYVVQDIYVYHHYMQDWIGDNGWGCA**FLQIICSWFKHQEYTEKSIPTHREIQQ---ALVDAGDKP

Parental  ATFVGSRQWIGSIEVQLVLNQLIGITSKILFVSQGSEMASQGRALANHFQSEGTPVMIG-GGVLAHTILG
          ATFVGS.Q.IGSIEVQLVL.QL.GI..KILFVSQGSEMASQG..LANHFQSE.T.V.IG.GGVLA.TILG
Retrocopy ATFVGSLQ*IGSIEVQLVLSQLTGIN*KILFVSQGSEMASQGQELANHFQSEETSVIIG<GGVLAQTILG

Parental  VAWNEITGQIKFLILDPHYTGAEDLQVILEKGWCGWKGPDFWNKDAYYNLCLPQRPKMI
          VAW....GQIKFLILDPHYTGAE.LQVILEKG.CG.KGPDFWNK.AY.NLCLPQ.P.MI
Retrocopy VAWDKTIGQIKFLILDPHYTGAENLQVILEKG*CGGKGPDFWNKYAYDNLCLPQ*PNMI

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	0.04 RPM	11.89 RPM
SRP051959_heart	0.04 RPM	11.03 RPM
SRP051959_kidney	0.00 RPM	14.95 RPM
SRP051959_liver	0.00 RPM	12.63 RPM
SRP051959_lung	0.02 RPM	11.88 RPM
SRP051959_lymph_node	0.02 RPM	10.80 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.76 RPM
SRP051959_spleen	0.00 RPM	11.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3122 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3122 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3122 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005943	1 retrocopy	retro_cjac_3122 ,
Monodelphis domestica	ENSMODG00000004727	1 retrocopy	retro_mdom_709,
Otolemur garnettii	ENSOGAG00000014660	1 retrocopy	retro_ogar_1617,