RetrogeneDB ID:

retro_cjac_2032

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:21:37513880..37514228(+)
Located in intron of:ENSCJAG00000003083
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000019406
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2032
ATGGGGCTGTTTGGAAAAACCCAGGAGAAGCCACTTAAAGAACTGATCCATGAATGGTCATTGAAGATAAGAAAGGAAAT
GAGAGTTGTTGACAGGCAAATAAGGGATATCCAAAGAGAAGAAGAAAAAGTGAAACAATCTGTGAAAGATGCAGCCAAGA
AGGGCCAGAATGATGTCCGTGTAGTTCTGACCAAGGAGATGATCAGGTCAAGGAAGGCCATGAGCAAGCGGTATGCATCC
AAAGTGCACATGAACTCAGTGCTCATGGGGATGAAGAACCAGCTCATGGTCTTGTGAGTGGCTGGTTCCCTGCAGAAGAG
CACAGAAGTGATGAAGGCCATGCAGTCT

ORF - retro_cjac_2032 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.66 %
Parental protein coverage: 52.49 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGLFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCVVLAKEMIRS
MGLFGKTQEKP.KEL..EWSLKIRKEMRVVDRQIRDIQREEEKVK.SVKDAAKKGQ.DV.VVL.KEMIRS
RetrocopyMGLFGKTQEKPLKELIHEWSLKIRKEMRVVDRQIRDIQREEEKVKQSVKDAAKKGQNDVRVVLTKEMIRS
ParentalRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQS
RKA.SK.YASK.HMNSVLMGMKNQL.VL.VAGSLQKSTEVMKAMQS
RetrocopyRKAMSKRYASKVHMNSVLMGMKNQLMVL*VAGSLQKSTEVMKAMQS

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 .24 RPM 31 .42 RPM
SRP051959_heart 0 .18 RPM 29 .06 RPM
SRP051959_kidney 0 .44 RPM 34 .23 RPM
SRP051959_liver 0 .22 RPM 18 .65 RPM
SRP051959_lung 0 .31 RPM 28 .70 RPM
SRP051959_lymph_node 0 .53 RPM 16 .76 RPM
SRP051959_skeletal_muscle 0 .22 RPM 21 .07 RPM
SRP051959_spleen 0 .34 RPM 29 .66 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2032 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2032 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2032 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000074791 retrocopy
Callithrix jacchus ENSCJAG00000019406 2 retrocopies
retro_cjac_2032 , retro_cjac_2784,
Cavia porcellus ENSCPOG000000017231 retrocopy
Macropus eugenii ENSMEUG000000091111 retrocopy
Microcebus murinus ENSMICG000000054923 retrocopies
Mus musculus ENSMUSG000000531191 retrocopy
Oryctolagus cuniculus ENSOCUG000000292771 retrocopy
Ochotona princeps ENSOPRG000000021912 retrocopies
Sorex araneus ENSSARG000000089171 retrocopy
Tursiops truncatus ENSTTRG000000104001 retrocopy



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