RetrogeneDB ID:

retro_cjac_960

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:12:28966155..28966442(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CCDC167
Ensembl ID:ENSCJAG00000005622
Aliases:None
Description:coiled-coil domain containing 167 [Source:HGNC Symbol;Acc:21239]


Retrocopy-Parental alignment summary:






>retro_cjac_960
ACAAAAAAGAAGTGGGAGAATCTGGGTGTTGCTCTAGAGATCGATGGGCTAGAGAAGAAGCTGTCCCAGTGTCAGAGAGA
CCTAAAGGCCGTGAACTCCAGGCTCCACAGCGGGGAGCTGAGCCCAGAGGCCAGGAGGTCCCTGGAGAAGGAGAAAACAG
CCTAATGAGCAAAGCCTCCAACTACAAGAAGGAAGTGAAGTTGCTTTGGCAAGAGAACCAGAAGAACATGCTGCTCTCTG
TGGCCATCTTCATCCTTCTGACCCTCGTCTATGCCTACTGGACCATG

ORF - retro_cjac_960 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.63 %
Parental protein coverage: 98.97 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTKKKRENLGVALEIDGLEKKLSQCRRDLEAVNSRLHSRELSAEARRSLEKEK-NSLMSKASNYEKELKLL
TKKK.ENLGVALEIDGLEKKLSQC.RDL.AVNSRLHS.ELS.EARRSLEKEK.NSLMSKASNY.KE.KLL
RetrocopyTKKKWENLGVALEIDGLEKKLSQCQRDLKAVNSRLHSGELSPEARRSLEKEK<NSLMSKASNYKKEVKLL
ParentalRQENWKNMLLSLAIFILLTLIYAYWTM
.QEN.KNMLLS.AIFILLTL.YAYWTM
RetrocopyWQENQKNMLLSVAIFILLTLVYAYWTM

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 1 .15 RPM
SRP051959_heart 0 .00 RPM 0 .60 RPM
SRP051959_kidney 0 .00 RPM 0 .51 RPM
SRP051959_liver 0 .00 RPM 0 .67 RPM
SRP051959_lung 0 .00 RPM 0 .63 RPM
SRP051959_lymph_node 0 .02 RPM 1 .12 RPM
SRP051959_skeletal_muscle 0 .15 RPM 0 .31 RPM
SRP051959_spleen 0 .02 RPM 1 .18 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_960 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_960 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_960 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000120692 retrocopies
Canis familiaris ENSCAFG000000308351 retrocopy
Callithrix jacchus ENSCJAG00000005622 2 retrocopies
retro_cjac_3293, retro_cjac_960 ,
Felis catus ENSFCAG000000067451 retrocopy
Mus musculus ENSMUSG000000240181 retrocopy
Otolemur garnettii ENSOGAG000000009211 retrocopy
Pongo abelii ENSPPYG000000165631 retrocopy



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