RetrogeneDB ID: retro_cjac_2061

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:11604572..11605166(+)
• Located in intron of: ENSCJAG00000005418

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_2061
AAGTATATCTTTGTGTCACTGCTGTCCCGGGACAGTGTATATGAGCTGCTCAGGAGAGTCTGCACCCACCTATAGCCTTC
CAGCAAGAAGAGTCTAAGTGTAAGAGAATTTCCAGAGGAACCTGAGTCTCTGGAAGTCCTCATCCCTGAGATGAAGTGTA
GAAAGGTATGCCCTTCCTCCAGGTCCCTGTCTCTCCCAGACAACATGCTTCGTACTCCTCCAGCATCTGTGGACTCCACA
GACAGTTTCTTCCCCTCCAGGATGCCTCCAGGGCCTGAAAAGTCAAGAGCCCAAGTAGCCTCTGAAAATGGCAGGAGGTG
GGCATGGTCCATGCCGGGCTGGGGTCCTGCCTGCCCTAAGAAGATGCCGAACTGCTCTCCCACTGCAGAGAATGCTGTCT
GTGAGGAAGATGAGCTGGAGGAGGAGACTGGGAGCACTGGGGAGCTGAGGCTCTGGGATTACCAGCTCCTGAAGGTCTTC
TTTGTGCTGATCTGCATCCTGGTTGTGTCCTCATCTTATCTGGCGTTCCGTATTTCACAGCTAGAGCAGCAGTTATGCTC
CTTGAGTTGGGACAGCCCAGTCCCTGGGCATAGG

Alignment

ORF - retro_cjac_2061 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.46 %
• Parental protein coverage: 56.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KYIFVSLLSRDSVYELLRRVCTHLQPSSKKSLSVRQFPEEPESLEVLIPEMKWRKVCPSSRSLSLPDNMP
          KYIFVSLLSRDSVYELLRRVCTHL.PSSKKSLSVR.FPEEPESLEVLIPEMK.RKVCPSSRSLSLPDNM.
Retrocopy KYIFVSLLSRDSVYELLRRVCTHL*PSSKKSLSVREFPEEPESLEVLIPEMKCRKVCPSSRSLSLPDNML

Parental  RTPAASVDSTDSFFPSRTPPGPEKSRAQVASENGRRWAWPMPGWGPACPKKMPNCSPTAENAVCEEDELE
          RTP.ASVDSTDSFFPSR.PPGPEKSRAQVASENGRRWAW.MPGWGPACPKKMPNCSPTAENAVCEEDELE
Retrocopy RTPPASVDSTDSFFPSRMPPGPEKSRAQVASENGRRWAWSMPGWGPACPKKMPNCSPTAENAVCEEDELE

Parental  EETGSTGELRLWDYQLLKVFFVLICILVVSSSYLAFRISQLEQQLCSLSWDSPVPGHR
          EETGSTGELRLWDYQLLKVFFVLICILVVSSSYLAFRISQLEQQLCSLSWDSPVPGHR
Retrocopy EETGSTGELRLWDYQLLKVFFVLICILVVSSSYLAFRISQLEQQLCSLSWDSPVPGHR

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	0.11 RPM	0.62 RPM
SRP051959_heart	0.28 RPM	1.25 RPM
SRP051959_kidney	0.18 RPM	8.34 RPM
SRP051959_liver	0.13 RPM	0.30 RPM
SRP051959_lung	0.46 RPM	12.85 RPM
SRP051959_lymph_node	0.43 RPM	0.30 RPM
SRP051959_skeletal_muscle	0.15 RPM	0.44 RPM
SRP051959_spleen	0.32 RPM	0.15 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2061 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2061 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2061 has 0 orthologous retrocopies within eutheria group .

---

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,