RetrogeneDB ID:

retro_cjac_843

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:11:33788953..33791416(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SCAP
Ensembl ID:ENSCJAG00000002419
Aliases:None
Description:SREBF chaperone [Source:HGNC Symbol;Acc:30634]


Retrocopy-Parental alignment summary:






>retro_cjac_843
CCCCCTGAGGCCTGCCTGCCCTCAGCCAAGACAGTTGGGCAGCCAACACGTTATGAGCGGCAGCTGGCTGTGCAGCCGTC
CACACCCCACACCATCATGTTGCAGCCATCTTCCTTCCAAAAACTTCGACTCCCCAAGAGGCTGCATATTGTCTACTTCC
TGGCCCGCACCCGTCTGGCACAGTGCCTAATCATGGCTGGCACTGTTGTCTGGATTGGCATCCTGGTGTACACTGACCCA
GCAGGGCTGCACACCTACCTCGCTGCCCAGGTGATAGAACAGAGCCCACTGGGTGAGGGAGCCCTGGCTCCCCTGCCTGT
GCCTAGCGGCATGCTGCCTGCCAGCCACCCGACCCTGCCTTCCATCTTCCCACCTGATGCCACTAAGCTACCTGAGAACC
AGACGTTGCCAGGCTAGCCACCTGAGCGTGGAGGTCTGGCAGAGCTTGTCCATGACAGCCCAGTCCCAGAGGTAACCTGG
GGGACTGAGGATGAGAAACTTTGGAGGAAATTGTCCTTCCGCCACTGGCCGACACTATTCAGCTATTACAACATCACAAT
GGCCAAGAGGTACATCAGCCTGCTGCCTGTCATCCCAGTTACGCTCCGCCTGAACCCGAGGGAGGCCCTGGAGGGCCGGC
ACCCTCAGGACAGCCGTAGTGCCCGGACCCCGCCGGGACCTGTGCGGGCTGGGCACTGGGAGGAGGGACCCAAGGGCCCA
GGTGGGGTGCAGGCCCACGGAGACATCACGCTTTACAAGGTGGCGGTGCTGGGTCTGGCCGCGGGCATCGTACTGGTGCT
GCTGCTACTCTGCCTGTACCGCGTGCTGTGCCCGAGCAACTACGGGCAGCCGGGCGGTGGGCCGGGGCGGTGGAGGCGCG
GGGAGCTGCCCTGCGACGACTACGGCTACACACCACCAAGACAGAGATCGTTCCGCTGGTGCTGCGCAGCCACCTCATGG
ACATCGAGTGCCTGGCCAGTGATGGCATGCTGCTGGTGAGCTGTTGCCTGGCGGGCCACGTCTGCGTGTGGGACGCGCAG
ACTGGGGACTGCCTCACGCGCATCCCGCGCCCGGGGCAGCACCGAGACAGTGGCGTGGGCAGCGGGCTTGAGGCTCAGGA
GAGCTGGGAACGACTTTCAGATGGTGGGAAGGCTGGCCCAGAGGAGCCTGGGGACAGCCCTCCCCTGAGACACCGCCCCC
GGGGCCCTCCGCCGCCTTCCCTCTTCCGGGACCAGCCAGACCTCACCTGCTTAATCGACACCAACTTTTCCGCACAACCG
CAGCCCTCAAGAGTCCACTCAGCCCGAGCCCCAGCCCCGGGCGGTCTGTGGCCACACTCGGGACTCCCCAGGCTATGACT
TCAGCCGCCTGGTGCAGCGGGTGTACCAGGAAGAGGGGCTGGTGGCCGTCTGCACTCCAGCCCTGCGCCCACCCTCGCCT
GGGCCGGTGCTGCCCCAAGCCCCTGAGGACAAGGGTAGCTTCCCTGAGAAGGGCTCCCCTTCCCTTGCCTGGGCCCCCAG
CGTGGAGGGTTCCTTCTGGAGCTTGGAGCTGCAGGGTGGTCTCATCGTAGTGGGGCAGAGCAGCGGCCAGCTGGAGGTGT
GGGACGCCATTTAAGGAGTGCTGTGCTGCAGCAGTGAGGAGGTCTTCTCAGGCATCGCCGTTCTGGTCTTCCTGGACAAA
AGGATTGTGGCTGCGAGGCTCAACGGTTCCCTTGATTTCTTCTCCTTGGAGACCCACACTGCCCTTAGCCCCCTGCAGTT
TAGAGGGACCTCAGGGCAGGGCAGTTCCCCTGCCTCTCCGATATACAGCAGCAGTGACACAGTGGCCTGTCACCTGACCC
ACACAGTGCCCTGTGCACACCAGAAACCCATCACAGCCTTGAAAGCTGCTGCCGGGTGCTTGGTGACTGGGAGCCAAGAC
CACACGCTGAGAGTGTTCCGTCTGGAGGATTCGTGCTGCCTCTTCACCCTGCAGGGCCACTCAGGGGCCATCACCACTGT
GTACATCGACCAGACCATGGTACTGGCCAGTGGAGGACAAGATGGGGCCATCTGCCTGTGGGATGTACTTACTGGTAGGC
GGGTCAGCCACATGTTTGCTCACCGTGGGGATGTCACCTCCCTGACCTGTACCACCTCCTGCAACATCAGCAGTGGCCTG
GATGACCTCAGCAGCATCTTGGACTGCAGCATGGGCATCAAGTTCTACTCCATTCAGCAGGACCTTGGCTGTGGTGCAAG
CTTAGGTGTCATCTCAGACAATCTGCTGGTGAGCGGTGGCCAGGGCTGTGTCTCCTTTTGGGACCTAAACTAAGGGGACC
TGTTACAGACAGTCTACCTAGGGAAGAACAGTGAGGCCCAGCCTGCCCGACAGATCCTGGTGCTGGACAATGCTGCCATT
GTCTGCAACTTCGGCAGTGAGCTCAGCCTGGTGTATGTGCCCTCTGTGCTGGAGAAGCTGGAC

ORF - retro_cjac_843 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.5 %
Parental protein coverage: 90.83 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPPEACLPSAKPVGQPTRYERQLAVRPSTPHTITLQPSSFRNLRLPKRLRVVYFLARTRLAQRLIMAGTVV
PPEACLPSAK.VGQPTRYERQLAV.PSTPHTI.LQPSSF..LRLPKRL..VYFLARTRLAQ.LIMAGTVV
RetrocopyPPEACLPSAKTVGQPTRYERQLAVQPSTPHTIMLQPSSFQKLRLPKRLHIVYFLARTRLAQCLIMAGTVV
ParentalWIGILVYTDPAGLRTYLAAQVTEQSPLGEGALAPLPVPSGMLPANHPDPAFSIFPPDAPKLPENQTLPGE
WIGILVYTDPAGL.TYLAAQV.EQSPLGEGALAPLPVPSGMLPA.HP....SIFPPDA.KLPENQTLPG.
RetrocopyWIGILVYTDPAGLHTYLAAQVIEQSPLGEGALAPLPVPSGMLPASHPTLP-SIFPPDATKLPENQTLPG*
ParentalPPERGGPAEVVHDSPVPEVTWGPEDEELWRKLSFRHWPTLFSYYNITLAKRYISLVPVIPVTLGLNPREA
PPERGG.AE.VHDSPVPEVTWG.EDE.LWRKLSFRHWPTLFSYYNIT.AKRYISL.PVIPVTL.LNPREA
RetrocopyPPERGGLAELVHDSPVPEVTWGTEDEKLWRKLSFRHWPTLFSYYNITMAKRYISLLPVIPVTLRLNPREA
ParentalLEGRHPQDDRNAWPPPGPVPAGHWEAGPKGPGGVQAHGDVTLYKVAALGLAAGIVLVLLLLCLYRVLCPR
LEGRHPQD.R.A..PPGPV.AGHWE.GPKGPGGVQAHGD.TLYKVA.LGLAAGIVLVLLLLCLYRVLCP.
RetrocopyLEGRHPQDSRSARTPPGPVRAGHWEEGPKGPGGVQAHGDITLYKVAVLGLAAGIVLVLLLLCLYRVLCPS
ParentalNYGQPGGGPGRRRRGELPCDDYGYAPP-ETEIVPLVLRGHLMDIECLASDGMLLVSCCLAGHVCVWDAQT
NYGQPGGGPGR.RRGELPCDDYGY.PP..TEIVPLVLR.HLMDIECLASDGMLLVSCCLAGHVCVWDAQT
RetrocopyNYGQPGGGPGRWRRGELPCDDYGYTPP<KTEIVPLVLRSHLMDIECLASDGMLLVSCCLAGHVCVWDAQT
ParentalGDCLTRIPRPGQRRDSGVGSGLEAQESWERLSDGGKAGPEEPGDSPPLRHHPRGPPPPSLFGDQPDLTCL
GDCLTRIPRPGQ.RDSGVGSGLEAQESWERLSDGGKAGPEEPGDSPPLRH.PRGPPPPSLF.DQPDLTCL
RetrocopyGDCLTRIPRPGQHRDSGVGSGLEAQESWERLSDGGKAGPEEPGDSPPLRHRPRGPPPPSLFRDQPDLTCL
ParentalIDTNFSAQPQPS-EPTQPEPRHRAVCGRTRDSPGYDFSRLVQRVYQEEGLVAVCTPALRPPSPGPVLPKA
IDTNFSAQPQPS.E.TQPEP..RAVCG.TRDSPGYDFSRLVQRVYQEEGLVAVCTPALRPPSPGPVLP.A
RetrocopyIDTNFSAQPQPS>ESTQPEPQPRAVCGHTRDSPGYDFSRLVQRVYQEEGLVAVCTPALRPPSPGPVLPQA
ParentalPEDEGGSPEKGSPSLAWAPSAEGSIWSLELQGGLIVVGRSSGRLEVWDAIEGVLCCSSEEVSSGITALVF
PED.G..PEKGSPSLAWAPS.EGS.WSLELQGGLIVVG.SSG.LEVWDAI.GVLCCSSEEV.SGI..LVF
RetrocopyPEDKGSFPEKGSPSLAWAPSVEGSFWSLELQGGLIVVGQSSGQLEVWDAI*GVLCCSSEEVFSGIAVLVF
ParentalLDKRIVAARLNGSLDFFSLETHTALSPLQFRGTSGRGSSPASAMYSSSDTVACHLTHTVPCAHQKPITAL
LDKRIVAARLNGSLDFFSLETHTALSPLQFRGTSG.GSSPAS..YSSSDTVACHLTHTVPCAHQKPITAL
RetrocopyLDKRIVAARLNGSLDFFSLETHTALSPLQFRGTSGQGSSPASPIYSSSDTVACHLTHTVPCAHQKPITAL
ParentalKAAAGRLVTGSQDHTLRVFRLEDSCCLFTLQGHSGAITTVYIDQTMVLASGGQDGAICLWDVLTGSRVSH
KAAAG.LVTGSQDHTLRVFRLEDSCCLFTLQGHSGAITTVYIDQTMVLASGGQDGAICLWDVLTG.RVSH
RetrocopyKAAAGCLVTGSQDHTLRVFRLEDSCCLFTLQGHSGAITTVYIDQTMVLASGGQDGAICLWDVLTGRRVSH
ParentalMFAHRGDVTSLTCTTSCVISSGLDDLISIWDRSTGIKFYSIQQDLGCGASLGVISDNLLVTGGQGCVSFW
MFAHRGDVTSLTCTTSC.ISSGLDDL.SI.D.S.GIKFYSIQQDLGCGASLGVISDNLLV.GGQGCVSFW
RetrocopyMFAHRGDVTSLTCTTSCNISSGLDDLSSILDCSMGIKFYSIQQDLGCGASLGVISDNLLVSGGQGCVSFW
ParentalDLNYGDLLQTVYLGKNSEAQPARQILVLDNAAIVCNFGSELSLVYVPSVLEKLD
DLN.GDLLQTVYLGKNSEAQPARQILVLDNAAIVCNFGSELSLVYVPSVLEKLD
RetrocopyDLN*GDLLQTVYLGKNSEAQPARQILVLDNAAIVCNFGSELSLVYVPSVLEKLD

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 .02 RPM 17 .02 RPM
SRP051959_heart 0 .00 RPM 18 .28 RPM
SRP051959_kidney 0 .00 RPM 34 .41 RPM
SRP051959_liver 0 .00 RPM 14 .60 RPM
SRP051959_lung 0 .02 RPM 19 .78 RPM
SRP051959_lymph_node 0 .00 RPM 24 .70 RPM
SRP051959_skeletal_muscle 0 .02 RPM 15 .42 RPM
SRP051959_spleen 0 .02 RPM 23 .72 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_843 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_843 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_843 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 ENSCJAG00000002419 1 retrocopy
retro_cjac_843 ,




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