RetrogeneDB ID: retro_cjac_2346

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:68996904..68997618(+)
• Located in intron of: ENSCJAG00000003659

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM192
• Ensembl ID: ENSCJAG00000009198
• Aliases: None
• Description: transmembrane protein 192 [Source:HGNC Symbol;Acc:26775]

Sequence

>retro_cjac_2346
GGTTTCTTGGATGTCACTCAAAGTATTGAAGATGACTCACCTCTTGATGCCCAGCTTCTCTTATGTTACTCACCAAAAGC
TCATTTTAGACCCCGATTCTATCTTTTTTCTACAGTGATCATAGACAAAGATCTTCTCTTGTTTATTTATGTTGTGTTAT
TTTTGGCATTTTTAACAGATATAGTTTGTTCTTACCCTAATCTAAATGAGGACAGGTGCCCAGGAAACTACACAAACTCT
TAAAGTTCAAATGGTCATAATCCTTGGGAAAGTTATTTTTTGTTTTTTCCATGTACATCTTAAATGCTACATCCAGTATC
ACCATAGCGAAGTCAGAAACTGAGGCTATAACTTGATCCATCTACTGATGGATAAACCATCTCAGGTGGCATTAATGGTA
CACTTCACTGGCAACATACTTATTCTCTTCATACTGTGTTGCAGCATTTCTTCCTGCGGCCCAGCAGATTATATCTTTAT
CTCCTTCTGGCCACCCTGGAACTGATCTGTTCTCTGGTGTGTCTACTCATTTACACAGTGAAAATCTGGAAACTTAATAA
AGCTAAACCATATCCTGATGTACTTGAAGGAAAAGTCTATACTTAACCCAACAATGTTACCTTGCAGACTGGGTTCATAA
CTATTTGAAACATACAAGAAATTGTTGAAAAGCAAGAAGACATAATAATATATATGAAGTGACACAGTTGGCTT

Alignment

ORF - retro_cjac_2346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.13 %
• Parental protein coverage: 89.3 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSLDITQSIEDDPLLEAQLLPHHSLQAHFRPQFHPLPTVII-VNLLWFIHLVFVILAFLTGVLCSYPNPN
          G.LD.TQSIEDD..L.AQLL...S..AHFRP.F....TVII...LL.FI..V...LAFLT...CSYPN.N
Retrocopy GFLDVTQSIEDDSPLDAQLLLCYSPKAHFRPRFYLFSTVIIDKDLLLFIYVV-LFLAFLTDIVCSYPNLN

Parental  EDKCPGNYTNP-LKVQTVIILGK-VILWILHLLLECYLQYHHSKVRNRGYNLIYRSTRHLKRLGLMIHSS
          ED.CPGNYTN..LK......LGK.VI....H..L.CY.QYHHS.VRN.GYNLI...........LM.H..
Retrocopy EDRCPGNYTNS<LKFKWS*SLGK<VIFCFFHVHLKCYIQYHHSEVRN*GYNLIHLLMDKPSQVALMVHFT

Parental  GNTVLLLILC-MQHSFPEPGRLYLDLILALLALELICSLMCLLIYTVKIRKFNKAKPEPDILEEEKICAY
          GN...L.ILC..QH.F..P.RLYL.L.LA...LELICSL.CLLIYTVKI.K.NKAKP.PD.L.E.K....
Retrocopy GNILILFILC<LQHFFLRPSRLYLYLLLA--TLELICSLVCLLIYTVKIWKLNKAKPYPDVL-EGKVYT*

Parental  PSNITSETGFRTISSLEEIVEKQGDIIEYLKRHNAL
          P.N.T..TGF.TI....EIVEKQ.DII.Y.K.H..L
Retrocopy PNNVTLQTGFITI*NIQEIVEKQEDIIIYMK*HSWL

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	1.77 RPM	3.75 RPM
SRP051959_heart	0.84 RPM	5.46 RPM
SRP051959_kidney	1.31 RPM	11.65 RPM
SRP051959_liver	0.56 RPM	6.24 RPM
SRP051959_lung	1.55 RPM	4.93 RPM
SRP051959_lymph_node	1.37 RPM	5.07 RPM
SRP051959_skeletal_muscle	0.46 RPM	6.84 RPM
SRP051959_spleen	0.95 RPM	9.43 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2346 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2346 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2346 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009198	1 retrocopy	retro_cjac_2346 ,
Homo sapiens	ENSG00000170088	1 retrocopy	retro_hsap_3483,
Macaca mulatta	ENSMMUG00000021912	1 retrocopy	retro_mmul_1769,
Nomascus leucogenys	ENSNLEG00000006475	1 retrocopy	retro_nleu_2203,
Pongo abelii	ENSPPYG00000015175	1 retrocopy	retro_pabe_2878,
Pan troglodytes	ENSPTRG00000016571	1 retrocopy	retro_ptro_2357,
Ictidomys tridecemlineatus	ENSSTOG00000000402	1 retrocopy	retro_itri_1414,