RetrogeneDB ID: retro_cjac_3170

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:117245450..117246181(-)
• Located in intron of: ENSCJAG00000018085

Retrocopy information

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

Parental gene information

• Parental gene symbol: ODC1
• Ensembl ID: ENSCJAG00000006576
• Aliases: None
• Description: None

Sequence

>retro_cjac_3170
ATTCCTCTTGTCATATCCCTTCATGCAGTCAAATATAAATATATCGATAGCAGAGCCATCATGAAGACTCTCACTGCCAA
CAGGATAGGATTTAACTGCTAGCAAGGCTGAAATACAATTGGTGCCGATTCTGGGGATACCCCCAGAAAGGTTTATCTAT
GCAAATCCTTGCAAACGAATGTCTCAGATTTAAAACACTGCCAATAATGGAGTCCAGATGAGGATTTTTGGTGGTGATTT
CGAGTTGATGCCAGTTGCCAGAGCACACTCAAAGCAGAGTTGGTTTTTAAGATTGCAAATGATGATTCTAAAGCAATCAG
TTGCCTCAGTGTTAAAATTGGTGCCATGCTCAAAGCCAGCAGGCTTCTTTTGGAATGGGCAAAAGAGCTAAATATTGATG
CCACTAGTGTCAGCTTCCATGCAGGAAGTGGCTATACCAATCCTAAGACCTCCACCCAGGCAGCCTCCAATGTCCACTGT
GTCTCTGAAAGGGGAGTTGAGTTTGGTTTCAGCATCTAACTGCTTGATACTGGCAGTTGCTTTCCTGGATCTGACGATGT
GAGGCTTAAATGTGAAGTATTACCAGCGTAATCAACCCAGCATCAGACAAGTATTTTCCACCAGGCTCTAGAGTGAGAGT
TACAGCTCAGCCAGGCAGATATTCTATGCGGTATCAGCTTTCACTGCCAAAAAAAATCATATTAAAAGAACAAACAGGTT
CTGAACAGACC

Alignment

ORF - retro_cjac_3170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.3 %
• Parental protein coverage: 52.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LPRVMPFYAVK-CNDSRAIVNALAAIGTGFDC-ASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANN
          .P.V....AVK..N.S.A.........TG.D..ASK.EIQLV..LG.PPER.IYANPCK..SQI...ANN
Retrocopy IPLVISLHAVK>INISIAEPS*RLSLPTG*DLTASKAEIQLVPILGIPPERFIYANPCKRMSQI*NTANN

Parental  GVQMMTFDSEVELMKVARAHPK-AKLVLRIATDDSKAICRLSVKFGATLKTSRLLLERAKELNIDVIGVS
          GVQM..F....ELM.VARAH.K.A.LV..IA.DDSKAI..LSVK.GA.LK.SRLLLE.AKELNID...VS
Retrocopy GVQMRIFGGDFELMPVARAHSK<AELVFKIANDDSKAISCLSVKIGAMLKASRLLLEWAKELNIDATSVS

Parental  FHVGSGCTDPETFVQAITDARCVFDMGAEVGFSMYLLDIGGGFPGSEDVKLKFE-EITSVINPALDKYFP
          FH.GSG.T.P.T..QA.....CV...G.E.GFS..LLD.G..FPGS.DV.LK.E..ITSVINPA.DKYFP
Retrocopy FHAGSGYTNPKTSTQAASNVHCVSERGVEFGFSI*LLDTGSCFPGSDDVRLKCE<SITSVINPASDKYFP

Parental  SDSEVRIIAEPGRYYVASAFTLAVNIIAKKIVLKEQT
          ..S.VR..A.PGRY.......L...II.K.....EQT
Retrocopy PGSRVRVTAQPGRYSMRYQLSLPKKIILKEQTGSEQT

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	1.20 RPM	53.69 RPM
SRP051959_heart	0.88 RPM	36.13 RPM
SRP051959_kidney	0.84 RPM	33.52 RPM
SRP051959_liver	0.78 RPM	31.30 RPM
SRP051959_lung	1.25 RPM	42.85 RPM
SRP051959_lymph_node	1.46 RPM	26.80 RPM
SRP051959_skeletal_muscle	0.92 RPM	36.84 RPM
SRP051959_spleen	1.32 RPM	23.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3170 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3170 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3170 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3090
Macaca mulatta	retro_mmul_1645

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011415	1 retrocopy	retro_amel_414,
Bos taurus	ENSBTAG00000004256	1 retrocopy	retro_btau_552,
Callithrix jacchus	ENSCJAG00000006576	2 retrocopies	retro_cjac_3170 , retro_cjac_3857,
Dasypus novemcinctus	ENSDNOG00000018474	31 retrocopies	retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016, retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Myotis lucifugus	ENSMLUG00000010423	1 retrocopy	retro_mluc_281,
Macaca mulatta	ENSMMUG00000020441	2 retrocopies	retro_mmul_157, retro_mmul_1645,
Monodelphis domestica	ENSMODG00000014779	1 retrocopy	retro_mdom_262,
Nomascus leucogenys	ENSNLEG00000013820	1 retrocopy	retro_nleu_1119,
Pongo abelii	ENSPPYG00000012654	1 retrocopy	retro_pabe_3090,
Ictidomys tridecemlineatus	ENSSTOG00000000386	2 retrocopies	retro_itri_1751, retro_itri_801,