RetrogeneDB ID:

retro_cjac_2009

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:20:23108792..23109334(-)
Located in intron of:ENSCJAG00000015408
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ZCRB1
Ensembl ID:ENSCJAG00000017749
Aliases:None
Description:zinc finger CCHC-type and RNA binding motif 1 [Source:HGNC Symbol;Acc:29620]


Retrocopy-Parental alignment summary:






>retro_cjac_2009
ATGAGTGGTGAGTTGGCTCCAAGTAAAAGCACAGAGCATATATCCAATTTGCCTATTCCCTGACAATTAATAACTTATAC
TGGATATTTTTCAAGGATGACAAAGTTGTAAAGACTACTATGATGAAATATAAAGATACCAGGAAGAGTAAAGAGGTTGC
ATTTATTTTATTTTTGGATAAAAGAGTTTGTACAAAACAGTATCAGGGCAATAAACAACAGTTACTTGGTAAAGTGATAA
AAGCAAGGAACACAATTGACAACAGAAGAGTAGCTGAGTTCACCCAAAGGCAGGACTACTTTCATGAATTTAAGTGTTAT
ATTTGTGAGAAAAGTGAATAACTAAGTTATGCCTGTCTGAAAAATATGCTTGGAGAACGTGAGCCTCCAAAGAAGAAAGA
AAAAAAGAAAGTTCCTGAACCAGTAGAAGAAACTGAAGCAGAAGCAAGTGAAAGTTAAAGGGAGAATTCTGCTTTTGACA
GCCTTAATCAGGCCATAGCATTCTCGCGAGCCAAAACTGAGTAAGAAAAAAAAGAAGAAAAA

ORF - retro_cjac_2009 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.43 %
Parental protein coverage: 85.71 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSGGLAPSKSTVYVSNLP-FSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR
MSG.LAPSKST...SNLP..SLT.N.LY.IF.K..KVVK.T.MK.KDTRKSK.VAFILFLDK.....CT.
RetrocopyMSGELAPSKSTEHISNLP<YSLTINNLYWIFFKDDKVVKTTMMKYKDTRKSKEVAFILFLDK---RVCTK
ParentalAI--NNKQLFGRVIKASIAIDNGRAAEFIRRRNYFDKSKCYECGESGHLSYACPKNMLGEREPPKKKEKK
....N..QL.G.VIKA...IDN.R.AEF..R..YF...KCY.C..S..LSYAC.KNMLGEREPPKKKEKK
RetrocopyQYQGNKQQLLGKVIKARNTIDNRRVAEFTQRQDYFHEFKCYICEKSE*LSYACLKNMLGEREPPKKKEKK
ParentalKKKKAPEPEEEIEEVEESEDEGEDPALDSLSQAIAFQQAKIEEEQKKWK
K....PEP.EE..E.E.SE...E..A.DSL.QAIAF..AK.E.E.K..K
RetrocopyK---VPEPVEE-TEAEASES*RENSAFDSLNQAIAFSRAKTE*EKKEEK

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 .51 RPM 5 .66 RPM
SRP051959_heart 0 .47 RPM 12 .40 RPM
SRP051959_kidney 0 .16 RPM 13 .71 RPM
SRP051959_liver 0 .41 RPM 11 .00 RPM
SRP051959_lung 0 .62 RPM 11 .91 RPM
SRP051959_lymph_node 1 .12 RPM 13 .06 RPM
SRP051959_skeletal_muscle 0 .09 RPM 13 .04 RPM
SRP051959_spleen 0 .67 RPM 12 .96 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2009 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2009 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2009 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 20 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000191192 retrocopies
Choloepus hoffmanni ENSCHOG000000044901 retrocopy
Callithrix jacchus ENSCJAG00000017749 3 retrocopies
retro_cjac_2009 , retro_cjac_2662, retro_cjac_4174,
Cavia porcellus ENSCPOG000000145541 retrocopy
Dasypus novemcinctus ENSDNOG0000001010711 retrocopies
Equus caballus ENSECAG000000121741 retrocopy
Erinaceus europaeus ENSEEUG000000003971 retrocopy
Echinops telfairi ENSETEG000000193021 retrocopy
Gorilla gorilla ENSGGOG000000156471 retrocopy
Loxodonta africana ENSLAFG000000088472 retrocopies
Microcebus murinus ENSMICG000000174223 retrocopies
Myotis lucifugus ENSMLUG000000013323 retrocopies
Monodelphis domestica ENSMODG000000088931 retrocopy
Mus musculus ENSMUSG000000226351 retrocopy
Oryctolagus cuniculus ENSOCUG000000136642 retrocopies
Otolemur garnettii ENSOGAG000000131782 retrocopies
Ochotona princeps ENSOPRG000000110952 retrocopies
Procavia capensis ENSPCAG000000117492 retrocopies
Pan troglodytes ENSPTRG000000048381 retrocopy
Pteropus vampyrus ENSPVAG000000066512 retrocopies



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