RetrogeneDB ID:

retro_cjac_2877

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:7:50303673..50303975(+)
Located in intron of:ENSCJAG00000008499
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TXNDC17
Ensembl ID:ENSCJAG00000011150
Aliases:None
Description:thioredoxin domain containing 17 [Source:HGNC Symbol;Acc:28218]


Retrocopy-Parental alignment summary:






>retro_cjac_2877
ATGGCCCACTACGAGGATGTGAGTGTGCCTGGCTTCGAGGAGTTCAACCGGGCCGTGGAACAGCACAACGGCAAGACCAT
TTTCACCTCCTTTACGGGTTCTAAGGAAGCCGGAGGGAAAAGCTAGTGCCCGACTGCGTGCAGGCTGAACCAGTTGTACA
AGAGGGGCTGAAGCACGTTAGTGAAGGATGAGTGTTCATCCACTGCCAAGTAGGAGACAAGCCTTATTGGAACGATCCAA
AGAATGGCTTCAGAAAAAACTTGAAAGTAACAGCAGTGCCTACGCTACTTGTATGGACCACC

ORF - retro_cjac_2877 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.35 %
Parental protein coverage: 82.11 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMARYEEVSVSGFEEFNRAVKQHNGKTIFAYFTGSKDAGGKSWCP-DCVQAEPVVREGLKHVSEGCVFIYC
MA.YE.VSV.GFEEFNRAV.QHNGKTIF..FTGSK.AGGKS.CP.DCVQAEPVV.EGLKHVSEG.VFI.C
RetrocopyMAHYEDVSVPGFEEFNRAVEQHNGKTIFTSFTGSKEAGGKS*CP<DCVQAEPVVQEGLKHVSEG*VFIHC
ParentalQVGDKPYWKDPNNDFRKNLKVTAVPTLLKYGT
QVGDKPYW.DP.N.FRKNLKVTAVPTLL...T
RetrocopyQVGDKPYWNDPKNGFRKNLKVTAVPTLLVWTT

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 .42 RPM 15 .26 RPM
SRP051959_heart 0 .21 RPM 5 .79 RPM
SRP051959_kidney 0 .29 RPM 11 .69 RPM
SRP051959_liver 0 .19 RPM 10 .57 RPM
SRP051959_lung 0 .34 RPM 7 .14 RPM
SRP051959_lymph_node 0 .39 RPM 7 .40 RPM
SRP051959_skeletal_muscle 0 .11 RPM 5 .31 RPM
SRP051959_spleen 0 .25 RPM 8 .28 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2877 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2877 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2877 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 27 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000070384 retrocopies
Callithrix jacchus ENSCJAG00000011150 4 retrocopies
Cavia porcellus ENSCPOG000000028871 retrocopy
Equus caballus ENSECAG000000250061 retrocopy
Echinops telfairi ENSETEG000000019051 retrocopy
Felis catus ENSFCAG000000241431 retrocopy
Homo sapiens ENSG000001292352 retrocopies
Gorilla gorilla ENSGGOG000000030552 retrocopies
Macropus eugenii ENSMEUG000000089461 retrocopy
Microcebus murinus ENSMICG000000066202 retrocopies
Macaca mulatta ENSMMUG000000037882 retrocopies
Mustela putorius furoENSMPUG000000113382 retrocopies
Mus musculus ENSMUSG000000208033 retrocopies
Nomascus leucogenys ENSNLEG000000092302 retrocopies
Oryctolagus cuniculus ENSOCUG000000165571 retrocopy
Ochotona princeps ENSOPRG000000005092 retrocopies
Procavia capensis ENSPCAG000000037491 retrocopy
Pongo abelii ENSPPYG000000078801 retrocopy
Pan troglodytes ENSPTRG000000086442 retrocopies
Pteropus vampyrus ENSPVAG000000023991 retrocopy
Rattus norvegicus ENSRNOG000000140721 retrocopy
Sorex araneus ENSSARG000000065011 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000219862 retrocopies
Tupaia belangeri ENSTBEG000000005391 retrocopy
Tarsius syrichta ENSTSYG000000109962 retrocopies
Tursiops truncatus ENSTTRG000000120721 retrocopy
Vicugna pacos ENSVPAG000000015541 retrocopy



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