RetrogeneDB ID: retro_cjac_3074

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:54115580..54116354(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB40C
• Ensembl ID: ENSCJAG00000036629
• Aliases: None
• Description: RAB40C, member RAS oncogene family [Source:HGNC Symbol;Acc:18285]

Sequence

>retro_cjac_3074
GTGGGCAAGGGCGAGATCCTGGAGAGCTTGCAGGACGGCGCGGCCGAGTCCCCGTATGCCTACAGCAACGGAATCGACTA
CAAGACCATCACCGTCCTGCTGGAAGGCCAGCGCGTGAAGCTGGCGCTCTGGGACACGTCCGGCCGGGGCTGGTTTTGCA
CCATCTTGAGGTCCTACTCCAGGGGCGCTCAGGGGATCCTCCTGGTGTTTGACGTCACCAACCTCTGGACCTTTGACAGC
ATCGACTGCTGCATCAAGGAGATCGACGAGCATGCGCCCAGAGTCCCCCGGATCTTGGTTGGAAAGAGGCTGCACCTGTC
CTTCAAGCTGCGGAGTCCTAACGGAGCAGGCCGGCGCATTCGCAGAGAAGAAGTACATGACCTTTTTTGAGGTCAACCCC
CTGTGCAACTTCAACGTCATCGAGTCCTTCACGGAGCTGTCCCGCATCGTGCTCAGGCGGCACGACATGGAGAAGATCTG
GAGGCCCAATTGAGTGTTCAGCCTGCAGGGCCTCTGTTGCTGGGCCATCGCCTCGTGCACCTCGGGGCACCTCATCGACA
AGCTTCCACTGCCCGTCCCATCAAGCCACCTCAAGTCCTTCTCAGTGGCCAACGGCATGAACGCCATCATGATGCACGGC
CGCTCCTACTCCCTGGCCAGCGGGGACGGGGTGGTGGTAGCAAGGGCAACAGCCTTAAGAGGTCCAAGCCCATCCGCCAG
CCCCAGAGCCCCTCCCGTCCCCGAAACTGCTCACGGAGAAACTGTAATATCTCC

Alignment

ORF - retro_cjac_3074 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.84 %
• Parental protein coverage: 91.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY
          VGKGEILESLQDGAAESPYAYSNGIDYKT.T.LL.G.RVKL.LWDTSG.G.FCTI.RSYSRGAQGILLV.
Retrocopy VGKGEILESLQDGAAESPYAYSNGIDYKTITVLLEGQRVKLALWDTSGRGWFCTILRSYSRGAQGILLVF

Parental  DITNRWSFDGIDRWIKEIDEHAPGVPRILVGNRLHLAFKRQVP-TEQARAYAEKNCMTFFEVSPLCNFNV
          D.TN.W.FD.ID..IKEIDEHAP.VPRILVG.RLHL.FK...P.TEQA.A.AEK..MTFFEV.PLCNFNV
Retrocopy DVTNLWTFDSIDCCIKEIDEHAPRVPRILVGKRLHLSFKLRSP>TEQAGAFAEKKYMTFFEVNPLCNFNV

Parental  IESFTELSRIVLMRHGMEKIWRPNRVFSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHLKSFSMANGMNA
          IESFTELSRIVL.RH.MEKIWRPN.VFSLQ.LCC.AI.SCT..HLIDKLPLPV...SHLKSFS.ANGMNA
Retrocopy IESFTELSRIVLRRHDMEKIWRPN*VFSLQGLCCWAIASCTSGHLIDKLPLPVP-SSHLKSFSVANGMNA

Parental  VMMHGRSYSLASGAG-SGGSKGNSLKRSKSIRPPQSP--PQNCSRSNCKIS
          .MMHGRSYSLASG.G..GGSKGNSLKRSK.IR.PQSP..P.NCSR.NC.IS
Retrocopy IMMHGRSYSLASGDG<GGGSKGNSLKRSKPIRQPQSPSRPRNCSRRNCNIS

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	3.88 RPM
SRP051959_heart	0.00 RPM	2.98 RPM
SRP051959_kidney	0.00 RPM	3.26 RPM
SRP051959_liver	0.00 RPM	1.82 RPM
SRP051959_lung	0.00 RPM	3.25 RPM
SRP051959_lymph_node	0.00 RPM	3.13 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.94 RPM
SRP051959_spleen	0.00 RPM	2.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3074 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3074 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3074 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000036629	1 retrocopy	retro_cjac_3074 ,
Echinops telfairi	ENSETEG00000005311	1 retrocopy	retro_etel_2052,