RetrogeneDB ID:

retro_cjac_2410

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:4:13718588..13718946(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:VAMP7
Ensembl ID:ENSCJAG00000016289
Aliases:None
Description:vesicle-associated membrane protein 7 [Source:HGNC Symbol;Acc:11486]


Retrocopy-Parental alignment summary:






>retro_cjac_2410
ATGAATAGTGAGTTCTCGAGTGTCTTGGCTGCACAGCTGAAGCCTCACTCCGAGAATAAGGGCCTAGACAAAGTGATGGA
GACTCAAGCCCAAGTGGATGAAATGAAAGGAATTATGGTCAGAAACATAGATCTGGTAGCTCAGTGAGAAGAAAGATTGG
AATTATTGATTTACAAAACAGAAAAATCTCCTGGATTCTTCTGTCACCTTCAAAACTACTAGCAGAAATCTTGCCCGAGC
CACGTGTATGAAGAACCTCAAGCTCACTATCATCATTATCATCATATTAATTGTGTTCATCTATGTCATTGTCTCACCTC
TCTGTGGTGGATTTACATGGCCAAGCTACGCAAAGAAA

ORF - retro_cjac_2410 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.17 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMNSEFSSVLAAQLKHHSENKGLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLIDKTE-NLVDSSVT
MNSEFSSVLAAQLK.HSENKGLDKVMETQAQVDE.KGIMVRNIDLVAQ..ERLELLI.KTE.NL.DSSVT
RetrocopyMNSEFSSVLAAQLKPHSENKGLDKVMETQAQVDEMKGIMVRNIDLVAQ*EERLELLIYKTE>NLLDSSVT
ParentalFKTTSRNLARAMCMKNLKLTIIIIVISIVFIYIIVSPLCGGFTWPSCVKK
FKTTSRNLARA.CMKNLKLTIIII.I.IVFIY.IVSPLCGGFTWPS..KK
RetrocopyFKTTSRNLARATCMKNLKLTIIIIIILIVFIYVIVSPLCGGFTWPSYAKK

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 18 .33 RPM
SRP051959_heart 0 .00 RPM 18 .22 RPM
SRP051959_kidney 0 .02 RPM 33 .10 RPM
SRP051959_liver 0 .02 RPM 23 .87 RPM
SRP051959_lung 0 .00 RPM 23 .86 RPM
SRP051959_lymph_node 0 .00 RPM 17 .67 RPM
SRP051959_skeletal_muscle 0 .00 RPM 13 .87 RPM
SRP051959_spleen 0 .00 RPM 26 .41 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2410 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2410 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2410 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000016289 2 retrocopies
retro_cjac_1958, retro_cjac_2410 ,
Cavia porcellus ENSCPOG000000244051 retrocopy
Mus musculus ENSMUSG000000514121 retrocopy
Oryctolagus cuniculus ENSOCUG000000012701 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000250361 retrocopy



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