RetrogeneDB ID: retro_cjac_2748

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:103384059..103385260(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C18orf25
• Ensembl ID: ENSCJAG00000008285
• Aliases: None
• Description: chromosome 18 open reading frame 25 [Source:HGNC Symbol;Acc:28172]

Sequence

>retro_cjac_2748
ATGAAGATGGAGGAGTCAGTGGGAAAAGTCAGAGAACTCATTGAGTCCAAAGTCCCACCAAGTATATCTGAACAAGAGAC
AGAAAAGGAGGAAGATGGATCTGTAGAACTGGAATCTCAAATTTAGAAAGATAATGTAGCAGATTCTACAGTTCTTTCTT
CAATGCCTTGCTTGTTGATGGAGCTGAAAAGAGACTTGTCTGAGTCTCAGCATCCACAGAGAGACAAGCCTACAACTGGC
TGAGTTTCTGAGAGTGACTCCTCTAATTACTGCATGCTTTCCTCTTTCTCTAGGGGTCACCTGGCTGATTCAGATACGTT
GTCTTCCGCAGAAGACAATGAAACCTCTCAGGCAGAAACAGTGGTAGAAGGAGACTCTTCAGCAGTCTGGTGCCACAGTT
ACAAGCAAGTCTAGGTGGTCCAGATGGGAAAGTGAAACATCCACTATGACTGCCAAGGAAAACCGGCAATACAGTGATAA
ACAGAATGGCCGAGTCACCAGGGTTAAAGGTCATAGGAGCCAAAAGCACAAGGAGAGGATCAGGCTACTGAGGCACAAAC
AGAAAGCTGCTACAAGGAAGAAATACAATGGGCTGCAGGACAGTAGTACCAGTGATAGTGACCCTACTTGTGATTCAAGC
ATGAGCTCATCAGATGATAATGAAGAGGTTTCAAGGAGCAACAAGACAATCACTGCAGAGATACCAGATGGACCTCCAGC
TGTAGTTCATTATGATATGCCTGACACCAGCTCTGACCCAGAAGTGGCAAATGTGTACAATTTATTGGCAGCTGCAGTGG
TTCAAGAGGACAATAATTCTGGTAGGCGGCTAGGACACAGGCGCTAGCTGGAGAACCAGCCGGCTTCTAGAAGAGCTGAA
TACAGAGGCAGGTCATTTGGATCCAGGATTCCTAGCAAGTGACAAAACATTTGCCAGCAATGCACCACTCAATGAAAAAA
TTAATATTGTCTCTTCATATAGTGAAGTAGAGATTGTGGGAGTTCAGGAACATGCAAGATGTGTTCATCCTCGAGGTGGT
ATGATTAGTGTTGCTTCATGGAAGCATGGCTCAGGCACACATTATCTTAGCACCAGGCACACACAGTCATGGACTGCTGT
GAGTCCCAGCAGACTTGGACTTCACCAGCAGAAGTTGTTGAGCTTACCTTGGATGAGGTTAGCAGGCATAAATACCTACT
G

Alignment

ORF - retro_cjac_2748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKMEEAVGKVEELIESEALPKTSEQETAKEEDGSVELESQVQKDGVAESTVISSMPCLLMELRRDSSESQ
          MKMEE.VGKV.ELIES...P..SEQET.KEEDGSVELESQ..KD.VA.STV.SSMPCLLMEL.RD.SESQ
Retrocopy MKMEESVGKVRELIESKVPPSISEQETEKEEDGSVELESQI*KDNVADSTVLSSMPCLLMELKRDLSESQ

Parental  LASTESDKPTTGRVYESDSSNHCMLSPSSSGHLADSDTLSSAEENEPSQAETAVEGDPSGV-SGATVGRK
          ......DKPTTG.V.ESDSSN.CMLS..S.GHLADSDTL.S..E.........V....S...SGATV..K
Retrocopy --HPQRDKPTTG*VSESDSSNYCMLSSFSRGHLADSDTL-SSAEDNETSQAETVVEGDSSA>SGATVTSK

Parental  SRRSRSESETSTMAAKKNRQSSDKQNGRVAKVKGHRSQKHKERIRLLRQKREAAARKKYNLLQDSSTSDS
          SR.SR.ESETSTM.AK.NRQ.SDKQNGRV..VKGHRSQKHKERIRLLR.K..AA.RKKYN.LQDSSTSDS
Retrocopy SRWSRWESETSTMTAKENRQYSDKQNGRVTRVKGHRSQKHKERIRLLRHKQKAATRKKYNGLQDSSTSDS

Parental  DLTCDSSTSSSDDDEEVSGSSKTITAEIPDGPPVVAHYDMSDTSSDPEVVNVDNLLAAAVVQEHNNS-VG
          D.TCDSS.SSSDD.EEVS.S.KTITAEIPDGPP.V.HYDM.DTSSDPEV.NV.NLLAAAVVQE.NNS.VG
Retrocopy DPTCDSSMSSSDDNEEVSRSNKTITAEIPDGPPAVVHYDMPDTSSDPEVANVYNLLAAAVVQEDNNS>VG

Parental  GQDTGATWRTSGLLEELNAEAGHLDPGFLASDKTSAGNAPLNEEINIASSDSEVEIVGVQEHARCVHPRG
          G.DTGA.WRTS.LLEELN.EAGHLDPGFLASDKT.A.NAPLNE.INI.SS.SEVEIVGVQEHARCVHPRG
Retrocopy G*DTGASWRTSRLLEELNTEAGHLDPGFLASDKTFASNAPLNEKINIVSSYSEVEIVGVQEHARCVHPRG

Parental  GVIQSVSSWKHGSGTQYVSTRQTQSWTAVTP-QQTWASPAEVVDLTLDEDSRRKYLL
          G.I.SV.SWKHGSGT.Y.STR.TQSWTAV.P.QQTW.SPAEVV.LTLDE.SR.KYLL
Retrocopy GMI-SVASWKHGSGTHYLSTRHTQSWTAVSP<QQTWTSPAEVVELTLDEVSRHKYLL

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	9.96 RPM
SRP051959_heart	0.00 RPM	16.35 RPM
SRP051959_kidney	0.00 RPM	10.03 RPM
SRP051959_liver	0.00 RPM	6.28 RPM
SRP051959_lung	0.00 RPM	10.90 RPM
SRP051959_lymph_node	0.00 RPM	10.50 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.50 RPM
SRP051959_spleen	0.00 RPM	10.67 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2748 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2748 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2748 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2190
Macaca mulatta	retro_mmul_917

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008285	1 retrocopy	retro_cjac_2748 ,
Homo sapiens	ENSG00000152242	1 retrocopy	retro_hsap_2190,
Macaca mulatta	ENSMMUG00000011473	1 retrocopy	retro_mmul_917,
Nomascus leucogenys	ENSNLEG00000011251	1 retrocopy	retro_nleu_320,