RetrogeneDB ID:

retro_cjac_1680

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:18:28088560..28089187(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TTC33
Ensembl ID:ENSCJAG00000007398
Aliases:None
Description:tetratricopeptide repeat domain 33 [Source:HGNC Symbol;Acc:29959]


Retrocopy-Parental alignment summary:






>retro_cjac_1680
ATTCTTGAATGCCGTGCTGAGAAGAGTAAACAGCTGAAGGATGAAGGAGCCAGTTTGGCTGAAAATAAAAGATACCAGTA
GGCAGTTCAGAAGTGGGATGAAGTACTACAGTTAACTCCAAATCATGCTACCCTATATGAGATGAAATCACAGGTGCTAA
TGTCTCTGCATGAAATGTTCCCAGCAGTACCTGCAGCAGAAATCAGCGTGCAGCAAAATCCACATTCGTGGGAGTCTTGG
CAAACTTTGGGACATGCTCAACTTGGATTAGGAAAGATAATCCTGGCAATTCAAGTAGCCCTTCACATCTATCCAGTGAA
CCCTGAAATATGGAAAGAAGACCTCTCTTGGGCAAGAACACTCCAGGAGCAGCAGAAGGTAGCCCAGATGATTTTAAAAA
AAGTGAAGCACCAGCTGACGTAACACACTTTTCACCCAAGTCAATTCCAGACTATGACTCCAAAAGTGATGAGATTTATT
GCTGTTTGTGCGGCTATTGCTGAGAAACAGAAGACAGTTTCAGCAAATAAAACAATGGTTACTGTGTCCACTTCTGGGGC
CCTAGAGACTGTAACTGAAGAGGAAGATGGTGCTACACCACCAGATGGCTCTGTTTTTGTCAGAGCC

ORF - retro_cjac_1680 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.42 %
Parental protein coverage: 80.84 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalILEGCAEKSKQLKDEGASLAENKRYREAIQKWDEALQLTPNDATLYEMKSQVLMSLHEMFPAVHAAEMAV
ILE..AEKSKQLKDEGASLAENKRY..A.QKWDE.LQLTPN.ATLYEMKSQVLMSLHEMFPAV.AAE..V
RetrocopyILECRAEKSKQLKDEGASLAENKRYQ*AVQKWDEVLQLTPNHATLYEMKSQVLMSLHEMFPAVPAAEISV
ParentalQRNPHSWESWQTLGRAQLGLGEIILAIRSFQVALHIYPMNPEIWKEDLSWARTLQEQQKVAQRIKKSEAP
Q.NPHSWESWQTLG.AQLGLG.IILAI...QVALHIYP.NPEIWKEDLSWARTLQEQQKVAQ.I.K....
RetrocopyQQNPHSWESWQTLGHAQLGLGKIILAI---QVALHIYPVNPEIWKEDLSWARTLQEQQKVAQMILKKVKH
ParentalAEVTH-FLPKSIPDYDFESDEIVAVCAAIAEKEKTVSANKTMVIVSASGAVETVTEKEDGATPPDGSVFI
....H.F.P..............AVCAAIAEK.KTVSANKTMV.VS.SGA.ETVTE.EDGATPPDGSVF.
RetrocopyQLT*HTFHPSQFQTMTPKVMRFIAVCAAIAEKQKTVSANKTMVTVSTSGALETVTEEEDGATPPDGSVFV
ParentalKA
.A
RetrocopyRA

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 .20 RPM 23 .85 RPM
SRP051959_heart 0 .14 RPM 27 .87 RPM
SRP051959_kidney 0 .00 RPM 30 .84 RPM
SRP051959_liver 0 .19 RPM 18 .45 RPM
SRP051959_lung 0 .10 RPM 24 .97 RPM
SRP051959_lymph_node 0 .21 RPM 27 .05 RPM
SRP051959_skeletal_muscle 0 .04 RPM 30 .79 RPM
SRP051959_spleen 0 .06 RPM 28 .07 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1680 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1680 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1680 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000007398 1 retrocopy
retro_cjac_1680 ,
Otolemur garnettii ENSOGAG000000119461 retrocopy



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