RetrogeneDB ID: retro_cjac_2671

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:137739587..137740706(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM161B
• Ensembl ID: ENSCJAG00000010857
• Aliases: None
• Description: None

Sequence

>retro_cjac_2671
GCTGCTACAGTTGTGTATCTAGTAACTGAAGTCTACTACAATTTTTTGAAGCCTACACAGTAAATGACTATCAGCTTAGT
CTGGTGCCTGCTTGTTTTGTCTTTTGCAATCAAAGTTCTATTTTCATTAACTACACACTATTTTAAAGTAGAAGATGGTG
GTGAAAGATCTGTTTTTGTCACCTTTGGATTTTTTTTTGTCAAAGCAATGGCAGTATTGATTGTAACAGTAAATTTTCTG
GAATTTGGACTTGAAATAGGGTTTATAAATTTTTCAGACATTGCGGTGTAGTTTCTTGAAAAGCAAGGTTTAGAATCACA
GAGTCCTATTTCAAAACTTACTTTCGAATTTTTCCTGGCTATTTTCCATTCACTCATTGGGAATTTTTTGACATTTCCTG
GATTATGGCTGGCTCAAATGCATCTGGATGCCCTGAATTTGGCAACAGAAAAAATTACACAAAGTTACTTCATATCAACT
TTTTAGGACCTTTATTTATGGTTCTGCTCTGGGTAAAACCAATCACCAAAGACTACATTACGAACCCACCATTGGGTAAA
GAAAGTATCCCTTTAACGACAGAAGTCACATTCGATACTCTGTGACTCTGGTTAATAATCCTGCTGTGTGCTTTGCAGTT
GGCCATGACATGTAGTCACCTGCAAGCTTATTTAAATTTATCCCAAAAATGTGTGGATCAGATGAAGAAAGAAGCAGGGC
AAATAATACAGTTGAGCTACAGAAAATGGTGGCTCGAGTCTCTTATTACCTTTGTGTCATTGCACTGCAGTATGTGGCGC
CTCTGGTAATGCTGCTTCACACAAATCTGCTTTTGAAAACACTAGGTAATCATTCCCGGGGTATTTCTCCAGAATCTATC
TCTACCTTACTAGTGGATAATAGTCTGCTCTCCAATTCTGTTTATTCTGAATTACCATCAGCTGAAGGTAAGATGAAAGT
AACTGTTACACAAATAACAGTGGCATTGAGCAGCTTAAAAATATTTTTACTCCTCTTCTTTTTCGAGGACTTCTGTCTTT
TCTGACCTGGTGGACTGCTGCTTGCCTCTTTTCTACAAGCCTTTTTGGGTTTTTCTATCACCAGTATCTGACTGTGGCA

Alignment

ORF - retro_cjac_2671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.42 %
• Parental protein coverage: 76.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AATVVYIVTEVYYNFMKPTQEMNISLVWCLLVLSFAIKVLFSLTTHYFKVEDGGERSVCVTFGFFFFVKA
          AATVVY.VTEVYYNF.KPTQ.M.ISLVWCLLVLSFAIKVLFSLTTHYFKVEDGGERSV.VTFGFFF.VKA
Retrocopy AATVVYLVTEVYYNFLKPTQ*MTISLVWCLLVLSFAIKVLFSLTTHYFKVEDGGERSVFVTFGFFF-VKA

Parental  MAVLIVTENYLEFGLETGFTNFSDSAMQFLEKQGLESQSPVSKLTFKFFLAIFCSLIGAFLTFPGLRLAQ
          MAVLIVT.N.LEFGLE.GF.NFSD.A..FLEKQGLESQSP.SKLTF.FFLAIF.SLIG.FLTFPGL.LAQ
Retrocopy MAVLIVTVNFLEFGLEIGFINFSDIAV*FLEKQGLESQSPISKLTFEFFLAIFHSLIGNFLTFPGLWLAQ

Parental  MHLDALNLATEKITQT-LLHINFLAPLFMVLLWVKPITKDYIMNPPLGKESIPLMTEATFDTLRLWLIIL
          MHLDALNLATEKITQ..LLHINFL.PLFMVLLWVKPITKDYI.NPPLGKESIPL.TE.TFDTL.LWLIIL
Retrocopy MHLDALNLATEKITQS<LLHINFLGPLFMVLLWVKPITKDYITNPPLGKESIPLTTEVTFDTL*LWLIIL

Parental  LCALRLAMMRSHLQAYLNLAQKCVDQMKKEAGRI-STVELQKMVARVFYYLCVIALQYVAPLVMLLHTTL
          LCAL.LAM..SHLQAYLNL.QKCVDQMKKEAG.I..TVELQKMVARV.YYLCVIALQYVAPLVMLLHT.L
Retrocopy LCALQLAMTCSHLQAYLNLSQKCVDQMKKEAGQI<NTVELQKMVARVSYYLCVIALQYVAPLVMLLHTNL

Parental  LLKTLGNHSWGIYPESISTLPVDNSLLSNSVYSELPSAEGKMKVTVTQITVALSSLK-NIFTPLLFRGLL
          LLKTLGNHS.GI.PESISTL.VDNSLLSNSVYSELPSAEGKMKVTVTQITVALSSLK.NIFTPLLFRGLL
Retrocopy LLKTLGNHSRGISPESISTLLVDNSLLSNSVYSELPSAEGKMKVTVTQITVALSSLK<NIFTPLLFRGLL

Parental  SFLTWWIAACLFSTSLFGLFYHQYLTVA
          SFLTWW.AACLFSTSLFG.FYHQYLTVA
Retrocopy SFLTWWTAACLFSTSLFGFFYHQYLTVA

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	0.87 RPM	11.45 RPM
SRP051959_heart	0.72 RPM	8.49 RPM
SRP051959_kidney	1.75 RPM	14.71 RPM
SRP051959_liver	0.22 RPM	9.94 RPM
SRP051959_lung	2.33 RPM	10.70 RPM
SRP051959_lymph_node	1.83 RPM	15.39 RPM
SRP051959_skeletal_muscle	0.09 RPM	8.10 RPM
SRP051959_spleen	0.80 RPM	13.80 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2671 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2671 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2671 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010857	1 retrocopy	retro_cjac_2671 ,
Homo sapiens	ENSG00000164180	1 retrocopy	retro_hsap_560,
Gorilla gorilla	ENSGGOG00000005684	1 retrocopy	retro_ggor_506,
Macaca mulatta	ENSMMUG00000009319	1 retrocopy	retro_mmul_719,
Nomascus leucogenys	ENSNLEG00000013645	1 retrocopy	retro_nleu_2224,
Pan troglodytes	ENSPTRG00000017064	1 retrocopy	retro_ptro_419,
Rattus norvegicus	ENSRNOG00000032414	1 retrocopy	retro_rnor_1023,
Ictidomys tridecemlineatus	ENSSTOG00000011141	1 retrocopy	retro_itri_1420,
Ictidomys tridecemlineatus	ENSSTOG00000027831	2 retrocopies	retro_itri_1419, retro_itri_1787,