RetrogeneDB ID:

retro_cjac_1765

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:18671236..18671698(+)
Located in intron of:ENSCJAG00000018960
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NME1
Ensembl ID:ENSCJAG00000018395
Aliases:None
Description:nucleoside diphosphate kinase A [Source:RefSeq peptide;Acc:NP_001191805]


Retrocopy-Parental alignment summary:






>retro_cjac_1765
CGGACCAGGGCCAACCTCGAGCGCACGTTCATCGCCATCAAGCGGATGGCGTGCAGCGCAGCCTGGTGGGCAACATCATC
AAGCACTTCCAGCAGCAGGGGTTCACCTCGTGGCCATGAAGTTCCTCCTGGCCTCTGAGGAACAGCTGAAGCAGCACTAC
ATTGACCTGAAAGACCACCCATTCTTTCCCCAGGCTGGTGAAGTACTTGAACTCAGGGCTGGCCGTGACCATGGTCTGGG
AGGCACTGAATGTGGTGAAGACCCGCTGAGTGATGCTGGGGGGAAACCAATCCAGTGGCTTCTAAGCCACGTACCATTTG
TGGGGACTTCTGCATTCAGGTTGGCAGGAACATAATTTATGACAGTGACTCAGTAAAAAGTGCTAAAAAAGAAATCAGCC
TATGGTTTAAGCCTGAAGAAATTTTTGACTACAAGTCTTGTGCTCATCACAGGGTCCATGAA

ORF - retro_cjac_1765 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.85 %
Parental protein coverage: 57.68 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalRTMANLERTFIAIK-PDGVQRGLVGEIIKRFEQKGF-RLVAMKFLRASEEHLKQHYIDLKDRPFFPG-LV
RT.ANLERTFIAIK..DGVQR.LVG.IIK.F.Q.GF..LVAMKFL.ASEE.LKQHYIDLKD.PFFP..LV
RetrocopyRTRANLERTFIAIK<ADGVQRSLVGNIIKHFQQQGF<HLVAMKFLLASEEQLKQHYIDLKDHPFFPQ>LV
ParentalKYMNSGPVVAMVWEGLNVVKTGRVMLG-ETNPADSKPGTIRGDFCIQVGRNIIHGSDSVKSADKEISLWF
KY.NSG..V.MVWE.LNVVKT..VMLG.ETNP..SKP.TI.GDFCIQVGRNII..SDSVKSA.KEISLWF
RetrocopyKYLNSGLAVTMVWEALNVVKTR*VMLG>ETNPVASKPRTICGDFCIQVGRNIIYDSDSVKSAKKEISLWF
ParentalKPEELVDYKSCAHDWVYE
KPEE..DYKSCAH..V.E
RetrocopyKPEEIFDYKSCAHHRVHE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP051959_colon 0 .00 RPM 46 .68 RPM
SRP051959_heart 0 .00 RPM 39 .69 RPM
SRP051959_kidney 0 .04 RPM 68 .24 RPM
SRP051959_liver 0 .00 RPM 50 .62 RPM
SRP051959_lung 0 .05 RPM 25 .60 RPM
SRP051959_lymph_node 0 .00 RPM 38 .49 RPM
SRP051959_skeletal_muscle 0 .00 RPM 75 .19 RPM
SRP051959_spleen 0 .00 RPM 42 .14 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1765 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1765 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1765 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 10 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000080223 retrocopies
Callithrix jacchus ENSCJAG00000018395 5 retrocopies
Erinaceus europaeus ENSEEUG000000037832 retrocopies
Homo sapiens ENSG000000110521 retrocopy
Myotis lucifugus ENSMLUG000000169293 retrocopies
Macaca mulatta ENSMMUG000000019401 retrocopy
Rattus norvegicus ENSRNOG000000026718 retrocopies
Sarcophilus harrisii ENSSHAG000000144703 retrocopies
Sus scrofa ENSSSCG000000175911 retrocopy
Tupaia belangeri ENSTBEG000000130536 retrocopies



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