RetrogeneDB ID:

retro_cjac_1025

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:12:32987182..32989032(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KIAA1279
Ensembl ID:ENSCJAG00000012896
Aliases:None
Description:KIAA1279 [Source:HGNC Symbol;Acc:23419]


Retrocopy-Parental alignment summary:






>retro_cjac_1025
ATGGCGAACGTTCCGTGGGCCAAAGTCTGCGAGAAATTCCAGGCGGCGCTGGCCCTGTCGCTGGTGGAACTGCATAAAAA
TCCGGAGAAGGAACCGTACAAGTCCAAATACAGCACCCGAGCGATGCTGGAAGAGGTCAACGCGCTGCTCGGCCCGGCGC
CTGAGGACGAGGATAAGTCGTCTGAGGCAGATGACCTCCCGGGGGCGGATGACCACGTCCTGGTGCTACCGGCTGAGGTG
GTGGAGCCCGAGGGGCCGGTAGGCTAGCCAGCGGTGAGGCTGGGGGTCATCGAGCTCCATCTCGAGGTGAACCACATCGA
CACCGAGGAGCTGTCGGCGGGGTAGGAGCACCTGGTGAAATGCCTGCGGCTGCTGCGCAGGTACCGGCTCTGGCACGACT
GCATCTCCCTCTGCATCCAGAATAACCTGGGTATCTTGTTTTCTGAAAGAGAAGAAATTGAAACTACACAGGCTTACCTA
GAGTCAACAGAAGCACTATATAATCAATATATGAAAGAGGTTGGGAGTCCTCTTTATCCAACTGAATGTTTTCTTCCTGC
AGAAGAGAAACTTACTGAACAAGAGAGATCAAAAAGATTAGAAAAGGTTTATACTTATAACCTATATTACCTAGCTCAAG
TCTACCAGCATCTGGAAATGTTTGAGAGGGCTGCTCACTATTGCCACAGTACACTACAGCGCCAGCTTGAGCACAATGCC
TACCATCCTATAGAGTGGACTATCAATGCTGCTACCTTGTCACAGTTTTACATCAATAAGCTATGCTTTATGGAGGCCAG
GCACTGTTTATCAGCTGCTAATGTCATTTTTGGTCAAACTGGAAAGATCTCAGCCACAGAAGACACTCCTGAAGTTGAAG
GAGAAGTGCCAGAGCTTTATCATCAAAGAAAGGGGGAAATAATAAGATGCTGGATCACATATTGTTTGACTTTCATGCAG
AATGCCCAACTCTCTATGCAGGACAACATAGGAGAGCTTGACCTTGATAAACAGTCTGAACTTAGAGCTTTAAGGAAAAA
AGAACTGGATGAGTAAGAAAGCATTCGGAAAAAAGCTCTGCAGTTTGGAACTGGTGAACTGTGTGATGCCATCTCTGCAG
TAGAATAGAAAGTGAGCTACTTGAGACCTTTAGATTTTGTAGAAGCCAGAGAACTTTTCTTATTGGGTCAGCACTATGTC
TTTGAGGCCAAACAGTTCTTTCAGATTGATGGTAATGTCACTGACCATATTGAAGTTGTCCAAGACCACAGTGCTCTGTT
TAAGATGCTTGCATTCTTTGAAACTGACATGGAGAGACAGTGCAAGATGCATAAACGCAGAATAGCCATGCTAGAGCCCC
TAACTGTAGACCTGAATCCACAGTATTATCTGTTGGTCAACAGACAGATCCAGTTTGAAATTGCACATGCTTACTATGAT
ATGGATTTGAAGGTCGCCACTGCTGACAGGCTAAGGGACCCTGATTCACACATTGTAAAAAAAATAAATAATCTTAATAA
GTTAACACTGAGGTACTACCAGCTCTTCTTAGACTCTCTGAGAGACCCAAATAAAGTATTTCTGACCATATATGGGAAGA
TGTTCTTCGCCCCGCCATGTTAGCAAAGTTTCGAGTTGCCCATCTCTATGGCAAAATCATTACCGCAGATCCCAAGAAAG
AGCTGGAAAATATGGCAACATCATTGGAAGATTACAAATTTATTGTTGATTACTGTGAAAAGCATCCTGAGGCTGCCCAG
GAATTAGAAACTGAGCTAGAACTTAGTAAAGAGATGGTTAGTTTTCTCCCAACAAAAATGGAGAGATTCAGAACCAAGAT
GGCCCTGACT

ORF - retro_cjac_1025 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.19 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMANVPWAEVCEKFQAALALSRVELHKNPEKEPYKSKYSARAMLEEVKALLGPTSEDEDERPEADDCPGAD
MANVPWA.VCEKFQAALALS.VELHKNPEKEPYKSKYS.RAMLEEV.ALLGP..EDED...EADD.PGAD
RetrocopyMANVPWAKVCEKFQAALALSLVELHKNPEKEPYKSKYSTRAMLEEVNALLGPAPEDEDKSSEADDLPGAD
ParentalDHALGLPAEVVEPEGPVGQRAVRLAVIEFHLGVNHIDTEELSAGEEHLVKCLRLLRRYRLSHDCISLCIQ
DH.L.LPAEVVEPEGPVG..AVRL.VIE.HL.VNHIDTEELSAG.EHLVKCLRLLRRYRL.HDCISLCIQ
RetrocopyDHVLVLPAEVVEPEGPVG*PAVRLGVIELHLEVNHIDTEELSAG*EHLVKCLRLLRRYRLWHDCISLCIQ
ParentalAQNNLGILWSEREEIETAQAYLESSEALYNQYMKEVGSPPLDPTECFLPAEEKLTEQERSKRFEKVYTHN
..NNLGIL.SEREEIET.QAYLES.EALYNQYMKEVGSP.L.PTECFLPAEEKLTEQERSKR.EKVYT.N
Retrocopy--NNLGILFSEREEIETTQAYLESTEALYNQYMKEVGSP-LYPTECFLPAEEKLTEQERSKRLEKVYTYN
ParentalLYYLAQVYQHLEMFEKAAHYCHSTLKRQLEHNAYHPIEWAINAATLSQFYINKLCFMEARHCLSAANVIF
LYYLAQVYQHLEMFE.AAHYCHSTL.RQLEHNAYHPIEW.INAATLSQFYINKLCFMEARHCLSAANVIF
RetrocopyLYYLAQVYQHLEMFERAAHYCHSTLQRQLEHNAYHPIEWTINAATLSQFYINKLCFMEARHCLSAANVIF
ParentalGQTGKISATEDTPEAEGEVPELYHQRKGEIARCWIKYCLTLMQNAQLSMQDNIGELDLDKQSELRALRKK
GQTGKISATEDTPE.EGEVPELYHQRKGEI.RCWI.YCLT.MQNAQLSMQDNIGELDLDKQSELRALRKK
RetrocopyGQTGKISATEDTPEVEGEVPELYHQRKGEIIRCWITYCLTFMQNAQLSMQDNIGELDLDKQSELRALRKK
ParentalELDEEESIRKKAVQFGTGELCDAISAVEEKVSYLKPLDFEEARELFLLGQHYVFEAKQFFQIDGYVTDHI
ELDE.ESIRKKA.QFGTGELCDAISAVE.KVSYL.PLDF.EARELFLLGQHYVFEAKQFFQIDG.VTDHI
RetrocopyELDE*ESIRKKALQFGTGELCDAISAVE*KVSYLRPLDFVEARELFLLGQHYVFEAKQFFQIDGNVTDHI
ParentalEVVQDHSALFKVLAFFETDMERRCKMHKRRIAMLEPLTVDLNPQYYLLVNRQIQFEIAHAYYDMMDLKVT
EVVQDHSALFK.LAFFETDMER.CKMHKRRIAMLEPLTVDLNPQYYLLVNRQIQFEIAHAYYD.MDLKV.
RetrocopyEVVQDHSALFKMLAFFETDMERQCKMHKRRIAMLEPLTVDLNPQYYLLVNRQIQFEIAHAYYD-MDLKVA
ParentalIADRLRDPDSHIVKKINNLNKSALKYYQLFLDSLRDPNKVF-PEHIGEDVLRPAMLAKFRVASLYGKIIT
.ADRLRDPDSHIVKKINNLNK..L.YYQLFLDSLRDPNKVF...HI.EDVLRPAMLAKFRVA.LYGKIIT
RetrocopyTADRLRDPDSHIVKKINNLNKLTLRYYQLFLDSLRDPNKVF<SDHIWEDVLRPAMLAKFRVAHLYGKIIT
ParentalMDPKKELENLATSLEHYKFIVDYCEKHPEAAQEIEVELELSKEMVSLLPAKMERFRTKMALT
.DPKKELEN.ATSLE.YKFIVDYCEKHPEAAQE.E.ELELSKEMVS.LP.KMERFRTKMALT
RetrocopyADPKKELENMATSLEDYKFIVDYCEKHPEAAQELETELELSKEMVSFLPTKMERFRTKMALT

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 8 .43 RPM
SRP051959_heart 0 .21 RPM 18 .94 RPM
SRP051959_kidney 0 .04 RPM 19 .37 RPM
SRP051959_liver 0 .35 RPM 8 .75 RPM
SRP051959_lung 0 .11 RPM 14 .58 RPM
SRP051959_lymph_node 0 .05 RPM 10 .80 RPM
SRP051959_skeletal_muscle 0 .07 RPM 12 .43 RPM
SRP051959_spleen 0 .11 RPM 12 .25 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_1025 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1025 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1025 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 ENSCJAG00000012896 1 retrocopy
retro_cjac_1025 ,


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