RetrogeneDB ID:

retro_cjac_1863

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:160267869..160268306(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000004992
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1863
CTTCAACATCTCATTCACCTGGGAGTTCAACAGCAAGTTTCCAAGATGCCACCCAAAGGAAAAAGTGGTTCTGGAAAAGC
AGGGAAGCGGGGAGCAGCCTCTGGGAGTGACAGTGCTGACAAGAAGGCTCAAGGTCCCAAAGGTGGTGGCAGTGCAGTAA
AGGTCAGACACATTGTATGTGAAAAACATGGCAAAATCATGGAAGCCATGGAAACATTAAAGTCTGGGATGAGATTCAAT
GAAGTGGCCACACAGTATAGTGAAGTAAAGCCAGGCAAGGGGGTGACTAGGGTTGGATGACCAGAGGGTCCATGGTGGGA
CCATTTCAAGAGGCAGGATTTGCCTTGCCTCTAAGTGGGATGGATAAATCTGTGTTTATAGACCCACCAGTTATGACAAA
ATTTGGATATCATACTATTATGGTTGAAGGAAGAAAA

ORF - retro_cjac_1863 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.35 %
Parental protein coverage: 94.81 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVRQLEQFRVQQQVSKMPPKGKSGSGKAGKGGAASGSDSAEKKAQGPKGGGNAVKVRHILCEKHSKIMEAM
...L....VQQQVSKMPPKGKSGSGKAGK.GAASGSDSA.KKAQGPKGGG.AVKVRHI.CEKH.KIMEAM
RetrocopyLQHLIHLGVQQQVSKMPPKGKSGSGKAGKRGAASGSDSADKKAQGPKGGGSAVKVRHIVCEKHGKIMEAM
ParentalEKLKSGMRFNEVAAQYSE-DKARQGGDLGWMTRGSMVGPFQEAAFALPVSGMDKPVFTDPPVKTKFGYHI
E.LKSGMRFNEVA.QYSE..KARQGGD.GWMTRGSMVGPFQEA.FALP.SGMDK.VF.DPPV.TKFGYH.
RetrocopyETLKSGMRFNEVATQYSE<SKARQGGD*GWMTRGSMVGPFQEAGFALPLSGMDKSVFIDPPVMTKFGYHT
ParentalIMVEGRK
IMVEGRK
RetrocopyIMVEGRK

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 .09 RPM 1 .31 RPM
SRP051959_heart 0 .26 RPM 1 .84 RPM
SRP051959_kidney 0 .16 RPM 3 .00 RPM
SRP051959_liver 0 .22 RPM 2 .86 RPM
SRP051959_lung 0 .34 RPM 1 .61 RPM
SRP051959_lymph_node 0 .18 RPM 1 .71 RPM
SRP051959_skeletal_muscle 0 .39 RPM 1 .51 RPM
SRP051959_spleen 0 .36 RPM 1 .83 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1863 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1863 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1863 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 19 parental genes, and 59 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000058011 retrocopy
Canis familiaris ENSCAFG000000322301 retrocopy
Callithrix jacchus ENSCJAG00000004992 10 retrocopies
Cavia porcellus ENSCPOG000000114011 retrocopy
Dipodomys ordii ENSDORG000000069852 retrocopies
Felis catus ENSFCAG000000120365 retrocopies
Homo sapiens ENSG000001023093 retrocopies
Gorilla gorilla ENSGGOG000000160084 retrocopies
Loxodonta africana ENSLAFG000000182611 retrocopy
Macropus eugenii ENSMEUG000000036111 retrocopy
Microcebus murinus ENSMICG000000016404 retrocopies
Myotis lucifugus ENSMLUG000000120732 retrocopies
Mustela putorius furoENSMPUG000000052873 retrocopies
Mus musculus ENSMUSG000000794808 retrocopies
Nomascus leucogenys ENSNLEG000000181191 retrocopy
Oryctolagus cuniculus ENSOCUG000000087152 retrocopies
Pongo abelii ENSPPYG000000204602 retrocopies
Rattus norvegicus ENSRNOG000000500516 retrocopies
Sorex araneus ENSSARG000000037322 retrocopies



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