RetrogeneDB ID:

retro_cjac_1968

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:154267531..154267998(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS19
Ensembl ID:ENSCJAG00000020243
Aliases:None
Description:ribosomal protein S19 [Source:HGNC Symbol;Acc:10402]


Retrocopy-Parental alignment summary:






>retro_cjac_1968
CTTTTAGCGGGCTGACAGCATGGAGGCCACACAATGCCTGGAGTTACTCTAAAAGACTTAAACCAGTAGGAGTTTGTCAG
AGTTCTGGCAGCCTTTCTCAAAAAGTCCAGGAAGCTGAAATTCCCTGAATAGGTGGACACCATCAAGCTAGTCAAGCTCA
AAGAGCTTGCTTCCTATGATGAGAACTGGTTCTACACATGAGCTTCTTCCACAGCACAGCACCTGTACCTCTAGGGTGGC
ACTGCAGTTGGCTCCATGACCAAGGTCTACGGGGATGTCACAGTAACAGCATCATGCCAAGGCCACTTCAGCCGAGGCTT
CAAGAGTGTGGCCTGCTGGGTCCTCTGAGCCCTGGAGGGGCTGAAAATGGTGGGAAAGGACCAAGATGGGGGCTCCAAAC
TGACACCTTAGGGATGAGAGATCTGGACAGACTCACTGGACAGGTGGCAGCTGCCATCAAGAAGTAT

ORF - retro_cjac_1968 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.33 %
Parental protein coverage: 99.36 %
Number of stop codons detected: 6
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLSPGWQRGGRTMPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAAS
L..G.Q.GG.TMPGVT.KD.NQ.EFVR.LAAFLKKS.KLK.PE.VDT.KL.K.KELA.YDENWFYT.A.S
RetrocopyLLAG*QHGGHTMPGVTLKDLNQ*EFVRVLAAFLKKSRKLKFPE*VDTIKLVKLKELASYDENWFYT*ASS
ParentalTARHLYLRGGAGVGSMTKIYG-GRQRNGVMP-SHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTP-Q
TA.HLYL.GG..VGSMTK.YG.G...N..MP..HFSRG.KSVA..VL.ALEGLKMV.KDQDGG.KLTP..
RetrocopyTAQHLYL*GGTAVGSMTKVYG<GCHSNSIMP>GHFSRGFKSVACWVL*ALEGLKMVGKDQDGGSKLTP<L
ParentalGQRDLDRIAGQVAAANKKH
G.RDLDR..GQVAAA.KK.
RetrocopyGMRDLDRLTGQVAAAIKKY

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 96 .18 RPM
SRP051959_heart 0 .00 RPM 54 .01 RPM
SRP051959_kidney 0 .00 RPM 60 .21 RPM
SRP051959_liver 0 .02 RPM 101 .61 RPM
SRP051959_lung 0 .00 RPM 81 .06 RPM
SRP051959_lymph_node 0 .00 RPM 147 .14 RPM
SRP051959_skeletal_muscle 0 .00 RPM 70 .93 RPM
SRP051959_spleen 0 .00 RPM 106 .66 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1968 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1968 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1968 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3174
Pan troglodytes retro_ptro_2269
Pongo abelii retro_pabe_2636
Macaca mulatta retro_mmul_2007

Parental genes homology:
Parental genes homology involve 26 parental genes, and 135 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000044564 retrocopies
Bos taurus ENSBTAG000000119632 retrocopies
Canis familiaris ENSCAFG0000002848510 retrocopies
Callithrix jacchus ENSCJAG00000020243 5 retrocopies
Cavia porcellus ENSCPOG000000251401 retrocopy
Dasypus novemcinctus ENSDNOG000000023764 retrocopies
Equus caballus ENSECAG000000097382 retrocopies
Erinaceus europaeus ENSEEUG000000136144 retrocopies
Felis catus ENSFCAG000000081253 retrocopies
Homo sapiens ENSG000001053725 retrocopies
Gorilla gorilla ENSGGOG000000152794 retrocopies
Myotis lucifugus ENSMLUG000000061435 retrocopies
Macaca mulatta ENSMMUG000000134298 retrocopies
Monodelphis domestica ENSMODG000000100673 retrocopies
Mustela putorius furoENSMPUG000000071644 retrocopies
Mus musculus ENSMUSG0000004095215 retrocopies
Otolemur garnettii ENSOGAG000000262553 retrocopies
Pongo abelii ENSPPYG000000100297 retrocopies
Pan troglodytes ENSPTRG000000110376 retrocopies
Pteropus vampyrus ENSPVAG000000089804 retrocopies
Rattus norvegicus ENSRNOG000000481993 retrocopies
Sarcophilus harrisii ENSSHAG000000068311 retrocopy
Sus scrofa ENSSSCG000000030423 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000035023 retrocopies
Tupaia belangeri ENSTBEG0000000345721 retrocopies
Tursiops truncatus ENSTTRG000000082785 retrocopies



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