RetrogeneDB ID:

retro_cjac_580

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:86554704..86555794(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000003505
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CCT6A
Ensembl ID:ENSCJAG00000021279
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_580
GTTTCTGCCGCTGGAGACAGCAAGCTTACTAATGATGGCAATGTGCTGCTTCACGAAATGCAAATTCAGCACCCAACAGC
TTCCTTAATAGCAAAGGCAGCAACAGCCCAGGATGATAAAACTGGTGATGGTACGACTTCCAAAGTCCTAATCATTGGAG
AGCTGCTGAAACAAGCGGATCTCTACATTTCTGAAGACCTTCATCCCAGAATAATTACTGAAGGATTTGAAGCTGCAAAG
GCAAAGGCCCTTCAGTTTTTGGAGGAAGTCAAAGTAAGCAAAGAGATGGACAGGGAAACACATAGATGTGGCCCGAACAT
CTCTTCGTACTAAAGTTCATGCTGAACTTGCAGATGTCTTAACAGAGGCTGTAGTGGACTCCATTTTGGCCATTAAAAAA
CAAGATGAGGCTGTTGATCTCTTCATGATTGAGATCATGGAGATGAAACATAAATCTGAAACTGATACGAGCTTAATCAG
AGGGCTTGTTTTGGACCATGGAGCACGGCATCCTGAAATGAAGAAAAGGGTGGAAGATGCATACATCCTCACATGTAACG
TGTCACTAGAATATGAAAAAATGGAAGTGAATTCTGGCTTTTTTTTACAAGAGTGCAGAAGAGAGAGAAAAACTTGTAAA
AGCTGGAAGAAAATTCATTGAAGATAGAATAAAAAAATAATAGAACTGAAAAGGAAAGTCTGTGGTGATTCAGATAAAGG
ATTTGTTGTTAATCAAAAGGGAATTGACCCCTTTTCATTAGATGCTCTTTCAAAAGAAGGCACAGTCGCTCTGCTCAGAG
CTAAAAGGAGAAATATGGAGAGGGTGACTCTTGCTTGTGGTGGGGTAGCCCTGAATTCTTTTGACGACCTAAGTCCTGAC
CGCTTGGGACATGCAGGCCTTGTATATAAGTATACATTGGGAGAAGAGAAATTCACCTTTATTGAGAAATGTAACAACCC
TCGTTCTGTCACATTATTGATCAAAGGGCCAAATAAGCACACACTCACTCAGATCAAAGATGCAGTAAGGGATGGCTTGA
GGGCTGTCAAAAATGCTATCGATGATGGCTGTGTGGTTCCAGGTGCTGGC

ORF - retro_cjac_580 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.67 %
Parental protein coverage: 73.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalVSGAGDIKLTKDGNVLLHEMQIQHPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYVSEGLHPR
VS.AGD.KLT.DGNVLLHEMQIQHPTASLIAK.ATAQDD.TGDGTTS.VLIIGELLKQADLY.SE.LHPR
RetrocopyVSAAGDSKLTNDGNVLLHEMQIQHPTASLIAKAATAQDDKTGDGTTSKVLIIGELLKQADLYISEDLHPR
ParentalIITEGFEAAK-EKALQFLEEVKVSKEMDRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDEPV
IITEGFEAAK......F....K..K.......IDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDE.V
RetrocopyIITEGFEAAK>QRPFSFWRKSK*AKRWTGKH-IDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDEAV
ParentalDLFMIEIMEMKHKSETDTSLIRGLVLDHGARHPEMKKRVEDAYILTCNVSLEYEKTEVNSGFF-YKSAEE
DLFMIEIMEMKHKSETDTSLIRGLVLDHGARHPEMKKRVEDAYILTCNVSLEYEK.EVNSGFF.YKSAEE
RetrocopyDLFMIEIMEMKHKSETDTSLIRGLVLDHGARHPEMKKRVEDAYILTCNVSLEYEKMEVNSGFF>YKSAEE
ParentalREKLVKAERKFIEDRIKK-IIELKRKVCGDSDKGFVVINQKGIDPFSLDALSKEGIVALRRAKRRNMERL
REKLVKA.RKFIEDRIKK.IIELKRKVCGDSDKGFVV.NQKGIDPFSLDALSKEG.VAL.RAKRRNMER.
RetrocopyREKLVKAGRKFIEDRIKK<IIELKRKVCGDSDKGFVV-NQKGIDPFSLDALSKEGTVALLRAKRRNMERV
ParentalTLACGGVALNSFDDLSPDCLGHAGLVYEYTLGEEKFTFIEKCNNPRSVTLLIKGPNKHTLTQIKDAVRDG
TLACGGVALNSFDDLSPD.LGHAGLVY.YTLGEEKFTFIEKCNNPRSVTLLIKGPNKHTLTQIKDAVRDG
RetrocopyTLACGGVALNSFDDLSPDRLGHAGLVYKYTLGEEKFTFIEKCNNPRSVTLLIKGPNKHTLTQIKDAVRDG
ParentalLRAVKNAIDDGCVVPGAG
LRAVKNAIDDGCVVPGAG
RetrocopyLRAVKNAIDDGCVVPGAG

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 .04 RPM 60 .17 RPM
SRP051959_heart 0 .05 RPM 76 .44 RPM
SRP051959_kidney 0 .04 RPM 69 .35 RPM
SRP051959_liver 0 .11 RPM 119 .96 RPM
SRP051959_lung 0 .03 RPM 67 .40 RPM
SRP051959_lymph_node 0 .05 RPM 92 .44 RPM
SRP051959_skeletal_muscle 0 .13 RPM 125 .50 RPM
SRP051959_spleen 0 .04 RPM 80 .13 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_580 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_580 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_580 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000160771 retrocopy
retro_amel_855,
Canis familiaris ENSCAFG000000101491 retrocopy
retro_cfam_431,
Choloepus hoffmanni ENSCHOG000000006543 retrocopies
retro_chof_1183, retro_chof_1193, retro_chof_150,
Callithrix jacchus ENSCJAG00000021279 2 retrocopies
retro_cjac_1320, retro_cjac_580 ,
Dipodomys ordii ENSDORG000000012491 retrocopy
retro_dord_617,
Felis catus ENSFCAG000000276542 retrocopies
retro_fcat_1102, retro_fcat_320,
Homo sapiens ENSG000001467312 retrocopies
retro_hsap_2741, retro_hsap_3290,
Gorilla gorilla ENSGGOG000000114391 retrocopy
retro_ggor_133,
Loxodonta africana ENSLAFG000000127911 retrocopy
retro_lafr_808,
Macaca mulatta ENSMMUG000000152721 retrocopy
retro_mmul_2582,
Monodelphis domestica ENSMODG000000065651 retrocopy
retro_mdom_1330,
Nomascus leucogenys ENSNLEG000000156641 retrocopy
retro_nleu_1355,
Oryctolagus cuniculus ENSOCUG000000176741 retrocopy
retro_ocun_468,
Procavia capensis ENSPCAG000000155321 retrocopy
retro_pcap_263,
Pongo abelii ENSPPYG000000258201 retrocopy
retro_pabe_2719,
Pan troglodytes ENSPTRG000000192062 retrocopies
retro_ptro_1854, retro_ptro_2225,
Pteropus vampyrus ENSPVAG000000014211 retrocopy
retro_pvam_663,
Rattus norvegicus ENSRNOG000000009231 retrocopy
retro_rnor_2226,
Tursiops truncatus ENSTTRG000000151581 retrocopy
retro_ttru_1552,


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