RetrogeneDB ID:

retro_cjac_855

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:11:53787192..53788293(+)
Located in intron of:ENSCJAG00000014492
Retrocopy
information
Ensembl ID:ENSCJAG00000014543
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DRG1
Ensembl ID:ENSCJAG00000011009
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_855
ATGAGCAGCACCTTAGCTAAGATCGCGGAGATAGAAGCTGAGATGGCTCGGACTCAAAAGAACAAGGCCACAGCACACCA
CCTAGGGCTGCTTAAGGCTCGTCTTGCTAAGCTTCGTCGAGAACTCATTACTCCAAAGGGTGGTGGTGGTGGAGGTCCAG
GAGAAGGTTTTGATGTGGCCAAGACAGGTGATGCTCGAATTGGATTTGTTGGTTTTCCATCTGTGGGGAAGTCAACACTG
CTTAGTAACCTGGCAGGGGTGTATTCTGAGGTAGCAGCCTATTGAATTCACTACTCTGACCACCATGCCTGGTGTCATCA
GATACAAAGGTGCCAAGATCCAGCTCCTGGATCTCCCAGGTATCATTGAAAGTGCCAAGGATGGGAAAGGTAGAGGTCAT
CAAGTCATTGCAGTGGCCCGAACCTGTAACTTGATCCTGATTGTTTTGGATGTCCTGAAACCCTTGGGACATAAGAAGAT
AATTGAAAATGAACTGGAAGGCTTTGGCATTCGCTTGAACAGCAAACCCCCCAACATTGGCTTTAAGAAAAAGGACAAGG
GAGGCATTAATCTCACAGCTACTTGCCCCCAGAGTGAGCTGAATGCTGAAACTGTGAAAAGCATTCTGGCCAAATACAAG
ATTCATAATGCTGATGTGACTCTACGTAGTGATGCTACAGCTGTGACCTCATTGATGTGGTGGAAGGAAACAGAGTTTAT
ATCCCCTGTATCTATGTGTTAAATAAGATTGACCAAATCTCCATTGAGGAATTGGATATCATCTATAAGGTGCCTCACTG
TGTATTCATCTCTGCCCATCACTGTTGGAATTTTGATGACCTATTGGAAAAGATCTGGGACTATCTGAAACTAGTGAGAA
TTTACACCAAACCCAAAGGCCAGTTACCAGATTACATATCCCCAGTGGTGCTTCCTTACTCCAGGACCACAGTGGAGGAT
TTCTGCATGAAGATTCACAAAAATCTTATCAAAGAATTTAAATATGCTCTGGTCTGGGGTCTCTCTGTGAAACACAATCC
TCAGAAAGTGGGTAAAGACCATACGTTGGAGGATGAGGATGTCATTCAAATTGTGAAGAAG

ORF - retro_cjac_855 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.02 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMSSTLAKIAEIEAEMARTQKNKATAHHLGLLKARLAKLRRELITPKGGGGGGPGEGFDVAKTGDARIGFV
MSSTLAKIAEIEAEMARTQKNKATAHHLGLLKARLAKLRRELITPKGGGGGGPGEGFDVAKTGDARIGFV
RetrocopyMSSTLAKIAEIEAEMARTQKNKATAHHLGLLKARLAKLRRELITPKGGGGGGPGEGFDVAKTGDARIGFV
ParentalGFPSVGKSTLLSNLAGVYSEVAAY-EFTTLTTVPGVIRYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVA
GFPSVGKSTLLSNLAGVYSEVAAY.EFTTLTT.PGVIRYKGAKIQLLDLPGIIE.AKDGKGRG.QVIAVA
RetrocopyGFPSVGKSTLLSNLAGVYSEVAAY>EFTTLTTMPGVIRYKGAKIQLLDLPGIIESAKDGKGRGHQVIAVA
ParentalRTCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDKGGINLTATCPQSELDAETVKSIL
RTCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDKGGINLTATCPQSEL.AETVKSIL
RetrocopyRTCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDKGGINLTATCPQSELNAETVKSIL
ParentalAEYKIHNADVTLRSDATAD-DLIDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVPISAHHRWNF
A.YKIHNADVTLRSDATA..DLIDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCV.ISAHH.WNF
RetrocopyAKYKIHNADVTLRSDATAV<DLIDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVFISAHHCWNF
ParentalDDLLEKIWDYLKLVRIYTKPKGQLPDYTSPVVLPYSRTTVEDFCMKIHKNLIKEFKYALVWGLSVKHNPQ
DDLLEKIWDYLKLVRIYTKPKGQLPDY.SPVVLPYSRTTVEDFCMKIHKNLIKEFKYALVWGLSVKHNPQ
RetrocopyDDLLEKIWDYLKLVRIYTKPKGQLPDYISPVVLPYSRTTVEDFCMKIHKNLIKEFKYALVWGLSVKHNPQ
ParentalKVGKDHTLEDEDVIQIVKK
KVGKDHTLEDEDVIQIVKK
RetrocopyKVGKDHTLEDEDVIQIVKK

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 .02 RPM 12 .89 RPM
SRP051959_heart 0 .25 RPM 12 .47 RPM
SRP051959_kidney 0 .04 RPM 15 .18 RPM
SRP051959_liver 0 .04 RPM 12 .93 RPM
SRP051959_lung 0 .10 RPM 12 .97 RPM
SRP051959_lymph_node 0 .02 RPM 14 .47 RPM
SRP051959_skeletal_muscle 0 .02 RPM 17 .67 RPM
SRP051959_spleen 0 .00 RPM 15 .90 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_855 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_855 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_855 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000070401 retrocopy
retro_amel_1448,
Canis familiaris ENSCAFG000000326016 retrocopies
retro_cfam_1535, retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis ENSCING000000033051 retrocopy
retro_cint_1,
Callithrix jacchus ENSCJAG00000011009 4 retrocopies
retro_cjac_1104, retro_cjac_2246, retro_cjac_2606, retro_cjac_855 ,
Cavia porcellus ENSCPOG000000107911 retrocopy
retro_cpor_1401,
Ciona savignyi ENSCSAVG000000065031 retrocopy
retro_csav_10,
Dasypus novemcinctus ENSDNOG000000013121 retrocopy
retro_dnov_531,
Homo sapiens ENSG000001857211 retrocopy
retro_hsap_2231,
Gorilla gorilla ENSGGOG000000111851 retrocopy
retro_ggor_1665,
Myotis lucifugus ENSMLUG000000070331 retrocopy
retro_mluc_1447,
Macaca mulatta ENSMMUG000000190991 retrocopy
retro_mmul_999,
Mustela putorius furoENSMPUG000000128101 retrocopy
retro_mputfur_339,
Mus musculus ENSMUSG000000204571 retrocopy
retro_mmus_2366,
Nomascus leucogenys ENSNLEG000000270011 retrocopy
retro_nleu_2627,
Pan troglodytes ENSPTRG000000142721 retrocopy
retro_ptro_1578,
Ictidomys tridecemlineatus ENSSTOG000000141871 retrocopy
retro_itri_460,
Tarsius syrichta ENSTSYG000000101603 retrocopies
retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,


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