RetrogeneDB ID:

retro_cjac_3400

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01178089.1:9276..10859(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000004247
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPD1
Ensembl ID:ENSCJAG00000003990
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3400
CTTTTAGCCGATGCCGTAGCTGTTACAATGGGGCCAAAGGGAAGAATAGTGATTATTGAGCAAAGCTGGGGAAGTCCCAA
AGTAACAAAAGATGGTTTGACTGTTGCAAAGTCAATTGACTCAAAGGATAAATATAAAAATATTGGAGCTAAACTTGTTC
AAGATGTTGCCAATAACACAAATGAAGAGGCTGGGGATGGCACTACCACGGCTACTGTACTGGCACGCTCTATTGCCAAG
GAAGGCTTCGAGAAGATTAGCAAAGGTGCTAATCCAGTGGAAATCAGGAGAGGTGTGATGTTAGCTGTTGATGCTGTAAC
TGCCGAACTTAAAAAGCAGTCTAAACCTGTGACCACCCCTGAAGAAATTGCACAGGTTGCTACAATTTCTGCAAATGGAG
ACAAAGAAATTGGGAATATCATCTCTGATGCAATGAAAAAGGTTGGAAGAAAGGGTGTCATCACAGTAAAGGATGGAAAA
ACACTTAATGATGAATTAGAAATTATTGAAGGCATGAAGTTTGATCGAGGCTATATTTCTCCATACTTTATTAATACATC
AAAAGGTCAGAAATGTGAATTCCAGGATGCCTATGTTCTGTTGAGTGAAAAGAAAATTTCTAGTGTCCAGTCGATTGTAC
CTGCTCTTGAAATTGCCAATGCTCATCATAAGCCTTTGGTCATAATCGCTGAAGACGTTGATGGAGAAGCTCTAAGTACA
CTTGTCTTGAATAGGCTAAAGGTTGGTCTTCAGGTTGTGGCGGTCAAGGCTCCAGGGTTGCTGACAATAGAAAGAACCAA
CTTAAAGATATGGCTATTGCTACTGGTGGTGCAGTGTTTGGGGAAGAGGGATTGACCCTAAATCTTGAAGATGTTCAGCC
TCATGACTTAGAGAAAGTTGGAGAGGTCATTGTGACCAAAGATGATGCCATGCTCTTAAAAGGAAAAGGCGACAAGGCTC
AAATTGAAAAACGTATTCAAGAAATCATTGAGCAGCTAGATGTCACAACTAGTGAATGTGAAAAGGAAAAACTGAATGAA
CGGCTGGCAAAACTTTCAGATGGAGTAGCTGTGCTGAAGGTTGGTGGGACAAGTGATGTTGAAGTGAATGAAAAGAAAGA
CAGAGTTACAGATGCCCTTAATGCTACAAGAGCTGCTGTTGAAGAAGGCATTGTTTTGGGAGGGGGTTGTGCCCTGCTTT
GGTGTATTCCAGCCTTAGACTCATTGACTCCAGCTAATGAAGATCAACAAATTGGTATAGAAATTATTAAAAGAACACTC
AAAATTCCAGCAATGACCATTGCTAAGAATGCAGGTGTTGAAGAATCTTTGATAGTTGAGAAAATTATGCAAAGTTTCTC
AGAAGTTGGTTATGATGCTATGGCTGGAGATTTTGTGAATATGGTGGGAAAAGGGATTATTGACCCAACAAAGGTTGTGA
GAACTGCTTTATTGGATGCTGCTGGTGTGGCCTCTCTGTTAACTACAGCAGAAGTTGTAGTCACAGAAATTCCTAAAGAA
GAGAAAGACCCTGGAATGGGTGCAATGGGTGGAATGGGAGGTGGTATGGGAGGTGGCATGTTC

ORF - retro_cjac_3400 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.16 %
Parental protein coverage: 92.15 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLLADAVAVTMGPKGRTVIIEQSWGSPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTT
LLADAVAVTMGPKGR.VIIEQSWGSPKVTKDG.TVAKSID.KDKYKNIGAKLVQDVANNTNEEAGDGTTT
RetrocopyLLADAVAVTMGPKGRIVIIEQSWGSPKVTKDGLTVAKSIDSKDKYKNIGAKLVQDVANNTNEEAGDGTTT
ParentalATVLARSIAKEGFEKISKGANPVEIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNI
ATVLARSIAKEGFEKISKGANPVEIRRGVMLAVDAV.AELKKQSKPVTTPEEIAQVATISANGDKEIGNI
RetrocopyATVLARSIAKEGFEKISKGANPVEIRRGVMLAVDAVTAELKKQSKPVTTPEEIAQVATISANGDKEIGNI
ParentalISDAMKKVGRKGVITVKDGKTLNDELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQ
ISDAMKKVGRKGVITVKDGKTLNDELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQ
RetrocopyISDAMKKVGRKGVITVKDGKTLNDELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQ
ParentalSIVPALEIANAHRKPLVIIAEDVDGEALSTLVLNRLKVGLQVVAVKAPGF-GDNRKNQLKDMAIATGGAV
SIVPALEIANAH.KPLVIIAEDVDGEALSTLVLNRLKVGLQVVAVKAPG...DNRKNQLKDMAIATGGAV
RetrocopySIVPALEIANAHHKPLVIIAEDVDGEALSTLVLNRLKVGLQVVAVKAPGL<ADNRKNQLKDMAIATGGAV
ParentalFGEEGLTLNLEDVQPHDLGKVGEVIVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSEYEKEKLNERL
FGEEGLTLNLEDVQPHDL.KVGEVIVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSE.EKEKLNERL
RetrocopyFGEEGLTLNLEDVQPHDLEKVGEVIVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSECEKEKLNERL
ParentalAKLSDGVAVLKVGGTSDVEVNEKKDRVTDALNATRAAVEEGIVLGGGCALLRCIPALDSLTPANEDQKIG
AKLSDGVAVLKVGGTSDVEVNEKKDRVTDALNATRAAVEEGIVLGGGCALL.CIPALDSLTPANEDQ.IG
RetrocopyAKLSDGVAVLKVGGTSDVEVNEKKDRVTDALNATRAAVEEGIVLGGGCALLWCIPALDSLTPANEDQQIG
ParentalIEIIKRTLKIPAMTIAKNAGVEGSLIVEKIMQSSSEVGYDAMAGDFVNMVDKGIIDPTKVVRTALLDAAG
IEIIKRTLKIPAMTIAKNAGVE.SLIVEKIMQS.SEVGYDAMAGDFVNMV.KGIIDPTKVVRTALLDAAG
RetrocopyIEIIKRTLKIPAMTIAKNAGVEESLIVEKIMQSFSEVGYDAMAGDFVNMVGKGIIDPTKVVRTALLDAAG
ParentalVASLLTTAEVVVTEIPKEEKDPGMGAMGGMGGGMGGGMF
VASLLTTAEVVVTEIPKEEKDPGMGAMGGMGGGMGGGMF
RetrocopyVASLLTTAEVVVTEIPKEEKDPGMGAMGGMGGGMGGGMF

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 .09 RPM 61 .81 RPM
SRP051959_heart 0 .09 RPM 59 .55 RPM
SRP051959_kidney 0 .22 RPM 131 .50 RPM
SRP051959_liver 0 .22 RPM 191 .35 RPM
SRP051959_lung 0 .07 RPM 48 .36 RPM
SRP051959_lymph_node 0 .14 RPM 75 .59 RPM
SRP051959_skeletal_muscle 0 .00 RPM 48 .39 RPM
SRP051959_spleen 0 .15 RPM 61 .13 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3400 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3400 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3400 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 25 parental genes, and 94 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137701 retrocopy
Bos taurus ENSBTAG000000125861 retrocopy
Canis familiaris ENSCAFG000000108654 retrocopies
Choloepus hoffmanni ENSCHOG000000074015 retrocopies
Callithrix jacchus ENSCJAG00000003990 6 retrocopies
Dasypus novemcinctus ENSDNOG000000132263 retrocopies
Echinops telfairi ENSETEG000000091844 retrocopies
Homo sapiens ENSG000001443817 retrocopies
Gorilla gorilla ENSGGOG000000082676 retrocopies
Loxodonta africana ENSLAFG000000000531 retrocopy
Macropus eugenii ENSMEUG000000119872 retrocopies
Myotis lucifugus ENSMLUG000000008714 retrocopies
Macaca mulatta ENSMMUG000000104891 retrocopy
Monodelphis domestica ENSMODG000000122893 retrocopies
Mustela putorius furoENSMPUG000000078183 retrocopies
Mus musculus ENSMUSG000000259805 retrocopies
Nomascus leucogenys ENSNLEG000000068747 retrocopies
Otolemur garnettii ENSOGAG000000340535 retrocopies
Pongo abelii ENSPPYG000000130465 retrocopies
Pteropus vampyrus ENSPVAG000000083061 retrocopy
Rattus norvegicus ENSRNOG000000145259 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000284701 retrocopy
Tarsius syrichta ENSTSYG000000005136 retrocopies
Tursiops truncatus ENSTTRG000000034173 retrocopies
Xenopus tropicalis ENSXETG000000075091 retrocopy



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