RetrogeneDB ID:

retro_cjac_3659

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01192774.1:2820..3223(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TXNL4A
Ensembl ID:ENSCJAG00000010130
Aliases:None
Description:thioredoxin-like 4A [Source:HGNC Symbol;Acc:30551]


Retrocopy-Parental alignment summary:






>retro_cjac_3659
ATGTCACACACACTCCTGCACCTCCACAGCAGCTGGCAGGTGGACCAGCCCATCCTCCCAGAGGAGGACCACATGGTTGT
CATTCGCTTCTGCAATGACTGGGACTCCACATGCATGAAAATGGACAAGGTCTTGTACAGCATCATTGAGAAGGTTAAAG
ATTTTGCAGTTATTTTTCTTGTGGATATTACCAAAGTACCTGACTTCAACAAAATGTATGAGTTATATGATCCATGCACT
ATCAGGAACAAGCACATCATGATTGTCTTGGGGACTGGCAACAAGATTAACTGGGCAATGGAGGATAAGCAGGAGATGGT
GGATATTAGAGGGATCATGGACCATAGGGCCTTCAATGGAGGCACCTGGTCATGCCCTCAAAAACTACTCCATGAAGTAC
AAA

ORF - retro_cjac_3659 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.93 %
Parental protein coverage: 99.3 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFN
MS..L.HLH..WQVDQ.IL.EED..VVIRF..DWD.TCMKMD.VLYSI.EKVK.FAVI.LVDIT.VPDFN
RetrocopyMSHTLLHLHSSWQVDQPILPEEDHMVVIRFCNDWDSTCMKMDKVLYSIIEKVKDFAVIFLVDITKVPDFN
ParentalKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKG-RGLVVSPK-DYST
KMYELYDPCT.....RNKHIMI.LGTG..NKINWAMEDKQEMVDI.......A..G.R.LV...K..YS.
RetrocopyKMYELYDPCTI----RNKHIMIVLGTG--NKINWAMEDKQEMVDIRGIMDHRAFNG<RHLVMPSK<NYSM
ParentalKYR
KY.
RetrocopyKYK

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 6 .61 RPM
SRP051959_heart 0 .00 RPM 6 .51 RPM
SRP051959_kidney 0 .07 RPM 7 .17 RPM
SRP051959_liver 0 .00 RPM 7 .06 RPM
SRP051959_lung 0 .65 RPM 5 .25 RPM
SRP051959_lymph_node 0 .02 RPM 7 .12 RPM
SRP051959_skeletal_muscle 0 .02 RPM 11 .79 RPM
SRP051959_spleen 0 .02 RPM 6 .66 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3659 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3659 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3659 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000010130 2 retrocopies
retro_cjac_2805, retro_cjac_3659 ,
Homo sapiens ENSG000001417592 retrocopies
Gorilla gorilla ENSGGOG000000052852 retrocopies
Loxodonta africana ENSLAFG000000031901 retrocopy
Myotis lucifugus ENSMLUG000000091881 retrocopy
Macaca mulatta ENSMMUG000000016132 retrocopies
Nomascus leucogenys ENSNLEG000000083782 retrocopies
Otolemur garnettii ENSOGAG000000347531 retrocopy
Pan troglodytes ENSPTRG000000101361 retrocopy
Rattus norvegicus ENSRNOG000000175962 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000222771 retrocopy
Tarsius syrichta ENSTSYG000000094281 retrocopy



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