RetrogeneDB ID:

retro_cjac_1872

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:171464202..171464775(+)
Located in intron of:ENSCJAG00000018841
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL9
Ensembl ID:ENSCJAG00000000723
Aliases:None
Description:ribosomal protein L9 [Source:HGNC Symbol;Acc:10369]


Retrocopy-Parental alignment summary:






>retro_cjac_1872
ATAAAGATGATTCTCAGCAATCAGACTGCTGACATTCCAGAAAATGTCAACGTTACTCTGAAGGGATGCAGGGTCATCGT
GAAGGACCCCAGAGGAATGCTGTGGAGGGAGTTCCATCACATCAACGTAAAACTCAGTCCTCTTGGAAAGAAAAAAAAGA
GGCTCCAGGTTGACAAATGGTGGGTGACAGAAAGGAGCTGGCTACCATTGGGACTATTTGTAGTCATGGACCAAATATGA
TAAAGGGTGTTGCACTGGGCTTTCGTTACAAGATGAGGTCTGTGCATGCGCATTCCCCATCAACGTCGTTATCCAGGAGA
ACCGGTCTCTTGTTGAAATACGAAATTTCTTGGGTGAAATATATCTCCCCAGGGTTCAGATGAGGCCAGGTATTCCTTGT
TCAATATCTCAAGCCCAGAAAGAATAATAATCCTTGAAGGAAATGGCATTGAACTTGTTTCAAATTCAGCGGCTTTGATT
CAGCAAGCCACAACAGTTAAAAACAAGAATATCAGGAAATATTTGGATGGCGTCTCTGTCTCTGAAAAAGGAACTGTTCA
GCAGGGTGATGAA

ORF - retro_cjac_1872 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.46 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMKTILSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKWW-GNRKELAT
.K.ILSNQT.DIPENV..TLKG..VIVK.PRG.L.R.F.HINV.LS.LGKKKKRL.VDKWW.G.RKELAT
RetrocopyIKMILSNQTADIPENVNVTLKGCRVIVKDPRGMLWREFHHINVKLSPLGKKKKRLQVDKWW<GDRKELAT
ParentalVRTICSHVQNMIKGVTLGFRYKMRSVYAH-FPINVVIQENGSLVEIRNFLGEKYIRRVRMRPGVACSVSQ
..TICSH..NMIKGV.LGFRYKMRSV.AH.FPINVVIQEN.SLVEIRNFLGE.Y..RV.MRPG..CS.SQ
RetrocopyIGTICSHGPNMIKGVALGFRYKMRSVHAH<FPINVVIQENRSLVEIRNFLGEIYLPRVQMRPGIPCSISQ
ParentalAQKD-ELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIYVSEKGTVQQADE
AQK....ILEGN.IELVSNSAALIQQATTVKNK.IRK.LDG..VSEKGTVQQ.DE
RetrocopyAQKE<IIILEGNGIELVSNSAALIQQATTVKNKNIRKYLDGVSVSEKGTVQQGDE

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 217 .75 RPM
SRP051959_heart 1 .11 RPM 184 .86 RPM
SRP051959_kidney 0 .13 RPM 211 .30 RPM
SRP051959_liver 0 .00 RPM 289 .47 RPM
SRP051959_lung 0 .05 RPM 203 .70 RPM
SRP051959_lymph_node 0 .00 RPM 348 .82 RPM
SRP051959_skeletal_muscle 0 .22 RPM 188 .40 RPM
SRP051959_spleen 0 .00 RPM 294 .43 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1872 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1872 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1872 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 27 parental genes, and 520 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000073171 retrocopy
Ailuropoda melanoleuca ENSAMEG0000000318731 retrocopies
Bos taurus ENSBTAG000000145183 retrocopies
Canis familiaris ENSCAFG0000001600828 retrocopies
Callithrix jacchus ENSCJAG00000000723 29 retrocopies
Danio rerio ENSDARG000000373501 retrocopy
Dasypus novemcinctus ENSDNOG0000000741118 retrocopies
Equus caballus ENSECAG000000164897 retrocopies
Erinaceus europaeus ENSEEUG0000000439439 retrocopies
Felis catus ENSFCAG0000001228434 retrocopies
Homo sapiens ENSG0000016368228 retrocopies
Gorilla gorilla ENSGGOG0000002279926 retrocopies
Gadus morhua ENSGMOG000000010021 retrocopy
Loxodonta africana ENSLAFG0000001202138 retrocopies
Macropus eugenii ENSMEUG000000167228 retrocopies
Microcebus murinus ENSMICG0000001677818 retrocopies
Myotis lucifugus ENSMLUG0000000459734 retrocopies
Macaca mulatta ENSMMUG0000000855322 retrocopies
Monodelphis domestica ENSMODG000000205537 retrocopies
Nomascus leucogenys ENSNLEG0000001710026 retrocopies
Otolemur garnettii ENSOGAG0000000493520 retrocopies
Pongo abelii ENSPPYG0000001467510 retrocopies
Pteropus vampyrus ENSPVAG0000000091949 retrocopies
Sarcophilus harrisii ENSSHAG000000049188 retrocopies
Sus scrofa ENSSSCG0000002519215 retrocopies
Tupaia belangeri ENSTBEG0000000604218 retrocopies
Vicugna pacos ENSVPAG000000020231 retrocopy



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