RetrogeneDB ID:

retro_cjac_1597

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:17:43244079..43245256(-)
Located in intron of:ENSCJAG00000003018
Retrocopy
information
Ensembl ID:ENSCJAG00000003024
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:IDH3G
Ensembl ID:ENSCJAG00000011185
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1597
ATGGCACTGAAGGTAGCAACAGCCTCTGGCGGCGCTATGAAGGCAGTGCTCCGGCCAGCCCTTCTGTGAAGTGCCTGGGA
GGTTCTAGGTGCCCATGAGGCCCCCCTCGAAGAGCATCTCCTCACAACAAATGATTCCTCCATCAGCTAAGTATGGCGGG
CGGCACACATCGACCGTGATCCCTGGTGATGGCATCGGGCCAAAGCTCATGCTGCATGTGAAGTCTGTTTTCAGGCACGC
CTGTGTCGGGTGGACTTTGAAGAGGTGCACGTGAGTTCCAACCTTGATGAAGAAGACATTAGCAAAGCCATCATGGCCAT
CCGCCGGAACCATGTGGCCCCGAAGGGCAATATCAACACCAACCGTAATCTGCCACCATCCCACAAATCCCGAAACAACA
TCTTCCGCACCAGCCCGGACCTCTATGCCAACGTCATCCACTATAAGAGCCTGCCAGGTGTGGTGACCCGACACAAGGAC
ATAGACATCCTCATTGTCCGGGAGAACACGGAGGGTGAGTACAGCAGCCTGGAGCATGAGAGTGTGGCGGGAGTGGTGGA
GAGCCTGAAGATCATCACCAAGGCCAAGTCCCTACGCGTTGCCATATGCTTTCAAGCTGGCGCTGAAGAGCGGGCGCAAG
AAAGTGACGGCCATGTACAAGGCCAACATCATGAAACTGGGCAACAGGCTCTTCCTCCAATGCTGCAGGGAGGTAGCAGC
TGGTTACCCCCAGATCACTTTCAAGAACACGATTGTGGACAACACCACCATGCAGCTGGTGTCCTGGCCCCAGCAATTTG
ATGTCGTGGTGATGCCCAATCTCTATGGCAACCTGGTCAGCAATGTCTGCTCAGGACTGGTCGGAGGCCCAGGCCTTGTG
GCTGGGGCCAACTATGGCCATGTGTACACGGTGTTTGAAACAGCTACGAGGAACACTGGCAAGAGTATCGCCAATAAGAA
CATCGCCAACCCCACAGCCATCCTGCTGGCCAGCTGCATGATGCTGGATCACCTCAAGCTGCACTTCTACGCCACCTCCA
TCCGTAAGGCTGTCCTGGTGTCCATGGACAATGAGAATATGCACACTCCAGACATTGGGGGCCAGGGCATAACATCTGAG
GCCATCCAGGACATCATCAGCCACATCCGTGTCATCAATGGCCAGGCTGTGGAGGCC

ORF - retro_cjac_1597 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.11 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMALKVATAASGAAKAVLRPALFCRPWEVLGAYEAP-SRSSSSQQTIPPSAKYGGRHTVTMIPGDGIGPEL
MALKVATA..GA.KAVLRPAL....WEVLGA.EAP.S.S.SSQQ.IPPSAKYGGRHT.T.IPGDGIGP.L
RetrocopyMALKVATASGGAMKAVLRPALL*SAWEVLGAHEAP>SKSISSQQMIPPSAKYGGRHTSTVIPGDGIGPKL
ParentalMLHVKSVFRHACVP-VDFEEVHVSSNADEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTS
MLHVKSVFRHACV..VDFEEVHVSSN.DEEDI..AIMAIRRN.VA.KGNI.TN.NLPPSHKSRNNI.RTS
RetrocopyMLHVKSVFRHACVG<VDFEEVHVSSNLDEEDISKAIMAIRRNHVAPKGNINTNRNLPPSHKSRNNIFRTS
ParentalLDLYANVIHCKSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLA
.DLYANVIH.KSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLR.A...F...
RetrocopyPDLYANVIHYKSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRVA-ICFQAG
ParentalQE-SGRKKVTAVHKANIMKLGDGLFLQCCREVAAGYPQITFENMIVDNTTMQLVSRPQQFDVMVMPNLYG
.E.SGRKKVTA..KANIMKLG..LFLQCCREVAAGYPQITF.N.IVDNTTMQLVS.PQQFDV.VMPNLYG
RetrocopyAE>SGRKKVTAMYKANIMKLGNRLFLQCCREVAAGYPQITFKNTIVDNTTMQLVSWPQQFDVVVMPNLYG
ParentalNIVNNVCAGLVGGPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATS
N.V.NVC.GLVGGPGLVAGANYGHVY.VFETATRNTGKSIANKNIANPTA.LLASCMMLDHLKLH.YATS
RetrocopyNLVSNVCSGLVGGPGLVAGANYGHVYTVFETATRNTGKSIANKNIANPTAILLASCMMLDHLKLHFYATS
ParentalIRKAVLASMDNENMHTPDIGGQGTTSEAIQDIIRHIRVVNGRAVEA
IRKAVL.SMDNENMHTPDIGGQG.TSEAIQDII.HIRV.NG.AVEA
RetrocopyIRKAVLVSMDNENMHTPDIGGQGITSEAIQDIISHIRVINGQAVEA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 16 .22 RPM
SRP051959_heart 0 .18 RPM 30 .52 RPM
SRP051959_kidney 0 .00 RPM 35 .30 RPM
SRP051959_liver 0 .09 RPM 10 .98 RPM
SRP051959_lung 0 .39 RPM 15 .31 RPM
SRP051959_lymph_node 0 .00 RPM 15 .43 RPM
SRP051959_skeletal_muscle 0 .02 RPM 33 .67 RPM
SRP051959_spleen 0 .67 RPM 17 .23 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_1597 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1597 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1597 has 0 orthologous retrocopies within eutheria group .

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

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184661 retrocopy
retro_amel_1892,
Bos taurus ENSBTAG000000010591 retrocopy
retro_btau_1194,
Canis familiaris ENSCAFG000000192861 retrocopy
retro_cfam_1023,
Callithrix jacchus ENSCJAG00000011185 1 retrocopy
retro_cjac_1597 ,
Equus caballus ENSECAG000000185091 retrocopy
retro_ecab_941,
Homo sapiens ENSG000000678291 retrocopy
retro_hsap_759,
Latimeria chalumnae ENSLACG000000073651 retrocopy
retro_lcha_17,
Loxodonta africana ENSLAFG000000069041 retrocopy
retro_lafr_560,
Macropus eugenii ENSMEUG000000139341 retrocopy
retro_meug_203,
Myotis lucifugus ENSMLUG000000044571 retrocopy
retro_mluc_396,
Mustela putorius furoENSMPUG000000087811 retrocopy
retro_mputfur_644,
Mus musculus ENSMUSG000000020101 retrocopy
retro_mmus_134,
Nomascus leucogenys ENSNLEG000000135401 retrocopy
retro_nleu_394,
Otolemur garnettii ENSOGAG000000067351 retrocopy
retro_ogar_25,
Pteropus vampyrus ENSPVAG000000131631 retrocopy
retro_pvam_373,
Rattus norvegicus ENSRNOG000000372841 retrocopy
retro_rnor_209,
Sus scrofa ENSSSCG000000127831 retrocopy
retro_sscr_662,
Tursiops truncatus ENSTTRG000000117281 retrocopy
retro_ttru_848,


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