RetrogeneDB ID: retro_cjac_1828

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:98193032..98193264(+)
• Located in intron of: ENSCJAG00000016120

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM2
• Ensembl ID: ENSCJAG00000002601
• Aliases: None
• Description: LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:13940]

Sequence

>retro_cjac_1828
TTCTATTGTTTTCTCAAGTCCCTTGTGGGCAAGGATGTGGTTGTGGAACTCAAGAATGACCTGAGCATCTGTGGAACTCT
CCATTCTGTGGATCAGTTATCTCAGCATCAGACTAACTGACATCATTGTCACAGACCCTGAGAAATATCCTCACATTTTA
TCAGTGAAGAACTGCTTCATTCTGGGCTCAATGGTCCGATACGTGCAGTTGCCAGCAAACAAGGTCCACACA

Alignment

ORF - retro_cjac_1828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 81.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FYSFFKSLVGKDVVVELKNDLSICGTLHSVDQ-YLNIKLTDISVTDPEKYPHMLSVKNCFIRGSVVRYVQ
          FY.F.KSLVGKDVVVELKNDLSICGTLHSVDQ.YL.I.LTDI.VTDPEKYPH.LSVKNCFI.GS.VRYVQ
Retrocopy FYCFLKSLVGKDVVVELKNDLSICGTLHSVDQ>YLSIRLTDIIVTDPEKYPHILSVKNCFILGSMVRYVQ

Parental  LPADEVDT
          LPA..V.T
Retrocopy LPANKVHT

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	0.13 RPM	5.75 RPM
SRP051959_heart	0.16 RPM	4.00 RPM
SRP051959_kidney	0.24 RPM	4.77 RPM
SRP051959_liver	0.04 RPM	3.66 RPM
SRP051959_lung	0.28 RPM	5.24 RPM
SRP051959_lymph_node	0.11 RPM	8.47 RPM
SRP051959_skeletal_muscle	0.02 RPM	4.91 RPM
SRP051959_spleen	0.08 RPM	6.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1828 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1828 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1828 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3361
Pan troglodytes	retro_ptro_2284
Pongo abelii	retro_pabe_2765
Macaca mulatta	retro_mmul_2099

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002601	2 retrocopies	retro_cjac_1828 , retro_cjac_2088,
Felis catus	ENSFCAG00000004511	1 retrocopy	retro_fcat_309,
Macaca mulatta	ENSMMUG00000006832	3 retrocopies	retro_mmul_1389, retro_mmul_1875, retro_mmul_2099,
Mus musculus	ENSMUSG00000007050	1 retrocopy	retro_mmus_931,
Nomascus leucogenys	ENSNLEG00000006371	1 retrocopy	retro_nleu_960,
Ochotona princeps	ENSOPRG00000003668	2 retrocopies	retro_opri_250, retro_opri_917,
Pongo abelii	ENSPPYG00000016461	1 retrocopy	retro_pabe_2765,
Pan troglodytes	ENSPTRG00000017986	3 retrocopies	retro_ptro_1349, retro_ptro_2063, retro_ptro_2284,
Rattus norvegicus	ENSRNOG00000048725	1 retrocopy	retro_rnor_1463,
Ictidomys tridecemlineatus	ENSSTOG00000013144	1 retrocopy	retro_itri_189,