RetrogeneDB ID:

retro_cjac_1320

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:15:12375297..12376141(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CCT6A
Ensembl ID:ENSCJAG00000021279
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1320
GCATTCTTAATATCAAAAGTAGCAACAGCTCAAGATTATATAACCGGGGATGGTATGACTAACAATATCCTAATAACTAG
AGAGCTATTGAAGTAGGTGTACCTCTACATTTCTGAAGGCCTTCATCCCAGGATAATTACTGAAGGATTTGAGGCTGCAA
GGGTAAGGGCCTTTCCGTTCTTGGAACAAGTCAAAGTAAGCAGAGGGATAAACATAGAAACACTTAGACATGTGGCCAGA
ACATCTCTTAGTACTAAAGTTCATGCTGAACTTGCAGATGTCTTAACATAGGCTGTAATGGACTCCATTTTAACCATTAA
AAGACAAATGGAACCTGTTGATCTCTTCATATTTGAGATCATGGAGATGAAACATAAACCTGAAACTGATACAAGGTTAA
TTAGAGGGCTTGTTTTGGACCATGGAATATGGTGTCCTGATTTGAAGAAAATGGTGGAAGATGCATACATCCTCAAGTGT
CATGTGTCATTAGAATATGAAAAAAGGAAGCGAAATCTGGCTTTTTTATTTACAAGACCAAAGAAGAGAGAGAATACAAT
TACAAAATCGGAAAGAAAGTTCATTGAACATAGAGTTAAAAAATAATAAAACTAAAAAGGAAAGTCTGTGGTGAATCAGA
TAAAGGATTTGTTATTATCAAAAGTGAATTGAACTCTTTTCCTTAGATGTTCTTGCAAAAGAAGGCATACTAGCTCTACA
CAGAGCTGAAAGTAGAAATACAGAGAGTCTGACTCTTGATTATGGTGGGGTAGCTCTGATTTCTTTTGATGACCTAAATC
CTGACTGCTTAGGACATGCAGATCTTGTGTATGAGTATACATTG

ORF - retro_cjac_1320 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.43 %
Parental protein coverage: 56.4 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYVSEGLHPRIITEGFEAAKEKALQFLEEVKVSKEM
A.LI.KVATAQD.ITGDG.T.N.LI..ELLK...LY.SEGLHPRIITEGFEAA...A..FLE.VKVS...
RetrocopyAFLISKVATAQDYITGDGMTNNILITRELLK*VYLYISEGLHPRIITEGFEAARVRAFPFLEQVKVSRGI
ParentalDRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDEPVDLFMIEIMEMKHKSETDTSLIRGLVLD
..ETL..VARTSL.TKVHAELADVLT.AV.DSIL.IK.Q.EPVDLF..EIMEMKHK.ETDT.LIRGLVLD
RetrocopyNIETLRHVARTSLSTKVHAELADVLT*AVMDSILTIKRQMEPVDLFIFEIMEMKHKPETDTRLIRGLVLD
ParentalHGARHPEMKKRVEDAYILTCNVSLEYE-KTEVNSGFF-YKSAEERE-KLVKAERKFIEDRIK-KIIELKR
HG...P..KK.VEDAYIL.C.VSLEYE.K.E..SGFF.YK..EERE....K.ERKFIE.R.K.KII.LKR
RetrocopyHGIWCPDLKKMVEDAYILKCHVSLEYE<KKEAKSGFFIYKTKEERE>TITKSERKFIEHRVK<KIIKLKR
ParentalKVCGDSDKGFVVINQKGIDPF-SLDALSKEGIVALRRAKRRNMERLTLACGGVALNSFDDLSPDCLGHAG
KVCG.SDKGFV.I.......F.SLD.L.KEGI.AL.RA..RN.E.LTL..GGVAL.SFDDL.PDCLGHA.
RetrocopyKVCGESDKGFVIIKSE-LNSF<SLDVLAKEGILALHRAESRNTESLTLDYGGVALISFDDLNPDCLGHAD
ParentalLVYEYTL
LVYEYTL
RetrocopyLVYEYTL

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 .00 RPM 60 .17 RPM
SRP051959_heart 0 .00 RPM 76 .44 RPM
SRP051959_kidney 0 .00 RPM 69 .35 RPM
SRP051959_liver 0 .00 RPM 119 .96 RPM
SRP051959_lung 0 .00 RPM 67 .40 RPM
SRP051959_lymph_node 0 .00 RPM 92 .44 RPM
SRP051959_skeletal_muscle 0 .00 RPM 125 .50 RPM
SRP051959_spleen 0 .00 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_1320 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1320 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1320 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2741
Pan troglodytes retro_ptro_1854
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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