RetrogeneDB ID: retro_cjac_1618

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:74315902..74316635(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRAMD2
• Ensembl ID: ENSCJAG00000018524
• Aliases: None
• Description: GRAM domain containing 2 [Source:HGNC Symbol;Acc:27287]

Sequence

>retro_cjac_1618
GAATGTCTCCTTTGCAGTCTGCACTGCCCAGAAGGCTTGAAGGGTGAAGAGATAAAGAAATGTGGCCGAGAAGGGATACC
ACTGAATAAATACCACCAGCAATACCACAAGCTGTTTAAGGATGCTCCCTTGGAGGAAGTGGTTTCTCAAAGTGTGCTCC
CCTGCACTCCAGAGGGACCTCCTTCTTCAGGGCGGGCTCTGCATCTCCCCCAACTGGCTCTGCTTCCACGCCAGCCTCTT
TGGCAAGGATATCAAGGTGGTCTTCCCTGTGGTGTCTGTGCAAATGATCAAAAAACACAAGCTGGCACAGCTCCTTCCCG
ACGGAATGGCCGTCACCACCACCACCAGCCAGAAGTGTGTCTTCGTGTCACTGCTCTCCTGGGACAGTGTGTAGGGGCTG
CATAGGAGAGACTGCACCCACCTACAGCCTTCCAGCAAGAAGAGTTGAAGCATAAGAGAATTTCCAGAGGAATCTGAGTC
TCTGGAAGTCCTCATCCCTGAGATGAAGTGGAGAAAGGTATGCCCATCCTCTAGGTCCCTGTCTCTCCCGGACAACATGC
CTCGTACCCCTCCTGAATCTGTGGACTCCACAGTTTCCTTCCCCTCCAGGAAGCCTCCAGGGCCTGAAAAGTCAACAGCC
TAAGTAGCCTCTGAAAATGGCAGGAGGTGGGCATGGCCCATGCCGGGCTGGGGTCCTGCTTGCCCTAAGAAGATGCCGAA
CTGCTCTCCCACC

Alignment

ORF - retro_cjac_1618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.99 %
• Parental protein coverage: 69.41 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPLDCSLHCPEGLKGEEIKKCGREGIPLNKYNQQYHKLFKDVPLEEVV-LKVCSCALQRDLLLQGRLYIS
          E.L.CSLHCPEGLKGEEIKKCGREGIPLNKY.QQYHKLFKD.PLEEVV.LKVCS.ALQRDLLLQG.L.IS
Retrocopy ECLLCSLHCPEGLKGEEIKKCGREGIPLNKYHQQYHKLFKDAPLEEVV>LKVCSPALQRDLLLQGGLCIS

Parental  PNWLCFHASLFGKDIKVVIPVVSVQMIKKHKLARLLPNGLAITTNTSQKYIFVSLLSRDSVYELLRRVCT
          PNWLCFHASLFGKDIKVV.PVVSVQMIKKHKLA.LLP.G.A.TT.TSQK..FVSLLS.DSV..L.RR.CT
Retrocopy PNWLCFHASLFGKDIKVVFPVVSVQMIKKHKLAQLLPDGMAVTTTTSQKCVFVSLLSWDSV*GLHRRDCT

Parental  HLQPSSKKSLSVRQFPEEPESLEVLIPEMKWRKVCPSSRSLSLPDNMPRTPAASVDSTDSFFPSRTPPGP
          HLQPSSKKS.S.R.FPEE.ESLEVLIPEMKWRKVCPSSRSLSLPDNMPRTP..SVDST.S.FPSR.PPGP
Retrocopy HLQPSSKKS*SIREFPEESESLEVLIPEMKWRKVCPSSRSLSLPDNMPRTPPESVDSTVS-FPSRKPPGP

Parental  EKSRAQVASENGRRWAWPMPGWGPACPKKMPNCSPT
          EKS.A.VASENGRRWAWPMPGWGPACPKKMPNCSPT
Retrocopy EKSTA*VASENGRRWAWPMPGWGPACPKKMPNCSPT

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	0.62 RPM
SRP051959_heart	0.00 RPM	1.25 RPM
SRP051959_kidney	0.00 RPM	8.34 RPM
SRP051959_liver	0.11 RPM	0.30 RPM
SRP051959_lung	0.08 RPM	12.85 RPM
SRP051959_lymph_node	0.00 RPM	0.30 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.44 RPM
SRP051959_spleen	0.11 RPM	0.15 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1618 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1618 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1618 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018524	3 retrocopies	retro_cjac_1618 , retro_cjac_2061, retro_cjac_2428,