RetrogeneDB ID:

retro_cjac_970

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:12:32999046..33000237(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000020705
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_970
GACTCCTCCTTCGAGGGTACCAGCGGCAATGGCTCCCCCACCCTGAACTCATCCACTTCGAGCAGCACGCAGGGCGACCC
TGCCTTCCCCGAGATGAATGGCAGCGGTGCCGTGGCCCCCATGGACTTCACCACAGCAGCGGAGGACCAGCTCATCAACC
TGTGTGACAAGCTCCCACCAGCCACGGCGCTCGGCACACCCTCCTACCCCTCCGACGGCTGCGGCACTGACGGGCTGCGG
AGCCGCGTCAAATACGGGGTGAAGACCAACCCCTGAGTCCCCCTCTTACAGCCCTGGGAGCTACGATTCCATCAAGACCG
AGGTCAGCGGCTGCCCCTAGGACCTGACATAGGCCTGGCTTCCCGGCAGATGACGACGACGATGACCACGATGCCCATGA
GAACAATGACAAGATTAACGAGTCTGAAGGCATGGACCCCTGAGCGCCTTAAGGCCTTAAACATGTTTGTGCGTCTCTTT
GTGGACGAGACTCTGGTGTGCCCATCTCCAAGCAGCCCAAAAAGAAGATCCAGGCTATCACTGAGTCGGGCAGTCGGCAG
TTCCCCGAATTCCAGGAGTGAGCCCGCAAGCGCATCGGCACGTACCTCAAGTCCTGCCGCCGCATGAAGAAGAACTGCAT
GGAGATGACCAGACCCACGCCACCCCACCTGACCTCGGCCATGACAGAAAACATTCTGGCAGCTGCCTCTGAGAGCGAGA
CGAGAAAGGCAGCCAAGCGGATGCGCCTGGAGTTCTAACAATCCTCACGGGATGAGCCCGTAGCCCTGGATAAGCAGCAC
TCGCCGGACTTCGTAGCCATCACCCACTCCACCTACTCACTGCCCGCCTCCTCCTTCTCCCAGGACCCTGTGTACGCCAA
TGGCAGCCTCAACTACAGTTACGGCGGGTACTGGGCCTTGAGCAGCAACCTGCAGCCCCCTGCGTCCCCTCCAAACAGGA
AGCCACAGTAATGGGCCCACCGACCTCAACATGAAAGGCGGAGCCTCGACCACCTCCACCACCCCCACGCCCATCCCCTC
CAGCACCAGCACCAGCAGGCCCGTGCCCACCGCTCAGCTCAGCCCCACGGAGATCAGCGCCGTGCGGCAGCTCATCTCGG
GCTACCGGGAGTCTGCTGCCTTCCTGCTGCGCTCTGCAGACCAACTGGAAAACCTCATCCTACAGCAGAAC

ORF - retro_cjac_970 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.15 %
Parental protein coverage: 99.75 %
Number of stop codons detected: 4
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalDSSSESGSGNGSSTLNPSTSSSTQGDPAFPEMNGNGAVAPMDFTTAAEDQPINLCDKLPPATALGTPSYP
DSS.E..SGNGS.TLN.STSSSTQGDPAFPEMNG.GAVAPMDFTTAAEDQ.INLCDKLPPATALGTPSYP
RetrocopyDSSFEGTSGNGSPTLNSSTSSSTQGDPAFPEMNGSGAVAPMDFTTAAEDQLINLCDKLPPATALGTPSYP
ParentalSDGCGTDGLRSRVKYGVKT-TPESPPYSSGSYDSIKTEVSGCPEDLTVGRAP-TADDDDDDHDDHEDNDK
SDGCGTDGLRSRVKYGVKT.TPESP.YS.GSYDSIKTEVSGCP.DLT....P...DD.DDDHD.HE.NDK
RetrocopySDGCGTDGLRSRVKYGVKT>TPESPSYSPGSYDSIKTEVSGCP*DLT*AWLP>ADDD-DDDHDAHENNDK
ParentalMNDSEGMD-PERLKAFNMFVRLFVDENLDRMVPISKQP-KEKIQAIIESCSRQFPEFQERARKRIRTYLK
.N.SEGMD.PERLKA.NMFVRLFVDE.L....P....P.K.KIQAI.ES.SRQFPEFQE.ARKRI.TYLK
RetrocopyINESEGMD>PERLKALNMFVRLFVDETL--VCPSPSSP<KKKIQAITESGSRQFPEFQE*ARKRIGTYLK
ParentalSCRRMKKNGMEMTRPTPPHLTSAMAENILAAACESETRKAAKRMRLEIYQSSQDEPIALDKQHSRDSAAI
SCRRMKKN.MEMTRPTPPHLTSAM.ENILAAA.ESETRKAAKRMRLE..QSS.DEP.ALDKQHS.D..AI
RetrocopySCRRMKKNCMEMTRPTPPHLTSAMTENILAAASESETRKAAKRMRLEF*QSSRDEPVALDKQHSPDFVAI
ParentalTHSTYSLPASSYSQDPVYANGGLNYSYRGYGALSSNLQPPAS-LQTGNHSNGPTDLSMKGGASTTSTTPT
THSTYSLPASS.SQDPVYANG.LNYSY.GY.ALSSNLQPPAS.LQTG.HSNGPTDL.MKGGASTTSTTPT
RetrocopyTHSTYSLPASSFSQDPVYANGSLNYSYGGYWALSSNLQPPAS>LQTGSHSNGPTDLNMKGGASTTSTTPT
ParentalPTPSSTSTSRPVPTAQLSPTEISAVRQLIAGYRESAAFLLRSADELENLILQQN
P.PSSTSTSRPVPTAQLSPTEISAVRQLI.GYRESAAFLLRSAD.LENLILQQN
RetrocopyPIPSSTSTSRPVPTAQLSPTEISAVRQLISGYRESAAFLLRSADQLENLILQQN

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 2 .33 RPM
SRP051959_heart 0 .04 RPM 0 .67 RPM
SRP051959_kidney 0 .00 RPM 1 .26 RPM
SRP051959_liver 0 .04 RPM 0 .54 RPM
SRP051959_lung 0 .02 RPM 1 .84 RPM
SRP051959_lymph_node 0 .00 RPM 0 .55 RPM
SRP051959_skeletal_muscle 0 .02 RPM 0 .31 RPM
SRP051959_spleen 0 .00 RPM 0 .88 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_970 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_970 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_970 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000020705 1 retrocopy
retro_cjac_970 ,


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