RetrogeneDB ID:

retro_cjac_1798

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:59779264..59781396(+)
Located in intron of:ENSCJAG00000010277
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:INTS7
Ensembl ID:ENSCJAG00000015814
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1798
ATGGCATCAAACTCAACTAAGTCTTTCCTGGCAGATGCCGGCTATGGCAAACAGGAACTGGATGCCAACTCTGCCCTTGT
GGAATTGGACAAAGGCCTAAGATATGGCAAACTTGGTGAACAGTGTGAAGCAGGTGTTCGCTTTCCCAGGCTTTTTCAGA
AGTATCCATTCCCTGTTCTTATCAATTCTGCATTTCTAAAGTTAGCTGATGTTTTCAGAGTTGGAAATAATTTCCTGAGG
CTATGTGTTCTTAAAGTTACCCAATAAAGTGAGAAACATTTGGAGAAGATTCTGAATGTGGATGAATTTGTGAAGAGAAT
CTTTTCTGTAATTCATAGTAATGATCCTGTGGCAAGAGCCATCACACTCCGGATGTTGGGAAGTCTGGCATCAATCATTC
CTGAGAGGAAGAATGCTCATTATAGTATTCGTCAGAGTTTAGATTCACATGATAATGTAGAAGTTGAAGCCGCTGTTTTT
GCTGCCGCAAACTGCTCTGCACAGTCAAAGGATTTTGCTGTAGGAATCTGTAACAAAATCAGTGAAATGATTCAAGGTTT
AGTGACACCAGTAGACTTGAAGCTAAAATTGATACCCATCTTACAGCACATGCACCATGATGCAATCCTGGCTTCCAGAG
CTCATCAGCTTTTACAACAGCTGGTCACATCCTATCCATCCACCAAAATGGTGATCGTTTCTTTGCACACTTTCACTCTG
CTTGCAGCTTCATCTTTGGTTGATACACCTAAGCAGATTCAGCTTCTGTTGCAGTATTTGAAGAATGATCCCAGGAAAGC
AGTAAAGAGACTTGCTATTCAAGATTTGAAATTACTTGCTAATAAAACACCACATACTTGGAGTAAGGAGAACATTCAGG
CACTTTGTGGGTGTGCCCTCCAGACTCCTTATGACAGCTTCAAACTAGGGATGTTGTCTGTCCTTTCCACACTATCAGAG
ACCATCGCCATCAAACATTACTTCAGTATAGTTCCAGGAAATGTGAGTTCTTCTCCCAGATCTTCTGATTTAGTCAAATT
AGCCCAAGAGTGCTGTTACCATAATAACAGGGGCATTGCAGCTCATGGAGTTAGAGTCCTAACTAATATAACTGTTTCTT
GTCAAGAAAAAGATCTTTTGGCACTGGAACAGGATGCTGTCTTTGGCCTGGAATCCCCACTGGTACTTTGCAGTCAAGAT
GATAGTCCAGGTCCTCAGACCACTTTAAAGATTGCTCTAAACTGTAAGGTGAAGTTGGCCAAGGGCAGGCCCCATCTTAG
TTAGTAGTGGTTGAGACCTTGTTGACTCAGTTGCACAGTGCTCAGGATGCTGCCTGGATTTTGATGTGCCATTGTTTGGC
AGCCATTGCCATGCAGCTGCTGGTGCTGGGTGATGGGATGCTTGGTGACCTCATGGAGCTATACAAGGTGACTGGACGAT
CAGCCACAGACAAGCAACAAGAACTTCTGGTGAGTTTGGCTACTGTGATTTTGTAGCGAGTCAGAAGGCATTATCGGTGG
AAGTAACGGCAGTGATTAAGCAGCAGCTTGAAAGTGTCTCCAATGGATGGACTATATACTGTATTGCCAGACAGTCTTCC
AGAATGGGTAATCATGACATGGCCAAAGAGCTTTATCAGAGTTTGCTGACTCAGTTTGCCTCAGAACACTTCTACTTCTG
GCTAAATAGTCTGAAGGAGTTCTCACATGCAGAGCAGTGTCTCACTGGTTGCAAGAGGAAAACTATAGTTCAGCACTTTC
TTGCATTGCTGAGTCTTTAATATTCTATCACAAAAGGATTGCTTCCTTAGCAGCTAGTACACCACTGAATCCTTTAAGTT
TTCAATGTGAACTTGTAAAACTCAGGATTGACCTTCTACAAGACTTCTCTCAACTTATCTGTACTTGTAATAGCCTAAAG
ACAAGCCCCCACCTGCAATTGCCACAACAATTGCCATGACCCTAGGAAATGACCTTGAGAGGTGTGGTCGAATCTCCAGT
CAGATGAAACAGTCCGTGGAAGAATTTCGGAGCCTTGCTTCTCCATATGGGGATCTTTACCAGGCCTCTTTTGATGCTGA
CTCAGCAACTTTGAGGAACGTCGAACTACAGCAGCAGAGTTGTTTACTGATG

ORF - retro_cjac_1798 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.86 %
Parental protein coverage: 74.12 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMASNSTKSFLADAGYGEQELDANSALMELDKGLRSGKLGEQCEAVVRFPRLFQKYPFPILINSAFLKLAD
MASNSTKSFLADAGYG.QELDANSAL.ELDKGLR.GKLGEQCEA.VRFPRLFQKYPFP.LINSAFLKLAD
RetrocopyMASNSTKSFLADAGYGKQELDANSALVELDKGLRYGKLGEQCEAGVRFPRLFQKYPFPVLINSAFLKLAD
ParentalVFRVGNNFLRLCVLKVTQQSEKHLEKILNVDEFVKRIFSVIHSNDPVARAITLRMLGSLASIIPERKNAH
VFRVGNNFLRLCVLKVTQ.SEKHLEKILNVDEFVKRIFSVIHSNDPVARAITLRMLGSLASIIPERKNAH
RetrocopyVFRVGNNFLRLCVLKVTQ*SEKHLEKILNVDEFVKRIFSVIHSNDPVARAITLRMLGSLASIIPERKNAH
ParentalHSIRQSLDSHDNVEVEAAVFAAANFSAQSKDFAVGICNKISEMIQGLATPVDLKLKLIPILQHMHHDAIL
.SIRQSLDSHDNVEVEAAVFAAAN.SAQSKDFAVGICNKISEMIQGL.TPVDLKLKLIPILQHMHHDAIL
RetrocopyYSIRQSLDSHDNVEVEAAVFAAANCSAQSKDFAVGICNKISEMIQGLVTPVDLKLKLIPILQHMHHDAIL
ParentalASSARQLLQQLVTSYPSTKMVIVSLHTFTLLAASSLVDTPKQIQLLLQYLKNDPRKAVKRLAIQDLKLLA
AS.A.QLLQQLVTSYPSTKMVIVSLHTFTLLAASSLVDTPKQIQLLLQYLKNDPRKAVKRLAIQDLKLLA
RetrocopyASRAHQLLQQLVTSYPSTKMVIVSLHTFTLLAASSLVDTPKQIQLLLQYLKNDPRKAVKRLAIQDLKLLA
ParentalNKTPHTWSKENIQVLCECALQTPYDSLKLGMLSVLSTLSGTIAIKHYFSIVPGNLSSSPRSSDLVKLAQE
NKTPHTWSKENIQ.LC.CALQTPYDS.KLGMLSVLSTLS.TIAIKHYFSIVPGN.SSSPRSSDLVKLAQE
RetrocopyNKTPHTWSKENIQALCGCALQTPYDSFKLGMLSVLSTLSETIAIKHYFSIVPGNVSSSPRSSDLVKLAQE
ParentalCCYHNNRGIAAHGVRVLTNITVSCQEKDLLALEQDAVFGLESLLVLCSQDDSPGAQATLKIALNCMVKLA
CCYHNNRGIAAHGVRVLTNITVSCQEKDLLALEQDAVFGLES.LVLCSQDDSPG.Q.TLKIALNC.VKLA
RetrocopyCCYHNNRGIAAHGVRVLTNITVSCQEKDLLALEQDAVFGLESPLVLCSQDDSPGPQTTLKIALNCKVKLA
ParentalKGRPHLS-QSVVETLLTQLHSAQDAARILMCHCLAAIAMQLPVLGDGMLGDLMELYKVIGRSATDKQQEL
KGRPHLS...VVETLLTQLHSAQDAA.ILMCHCLAAIAMQL.VLGDGMLGDLMELYKV.GRSATDKQQEL
RetrocopyKGRPHLS<LVVVETLLTQLHSAQDAAWILMCHCLAAIAMQLLVLGDGMLGDLMELYKVTGRSATDKQQEL
ParentalLVSLATVI-FVASQKALSVEVKAVIKQQLESVSNGWTVYRIARQASRMGNHDMAKELYQSLLTQVASEHF
LVSLATVI.FVASQKALSVEV.AVIKQQLESVSNGWT.Y.IARQ.SRMGNHDMAKELYQSLLTQ.ASEHF
RetrocopyLVSLATVI<FVASQKALSVEVTAVIKQQLESVSNGWTIYCIARQSSRMGNHDMAKELYQSLLTQFASEHF
ParentalYFWLNSLKEFSHAEQCLTG-LQEENYSSALSCIAESLKFYHKGIASLTAASTPLNPLSFQCEFVKLRIDL
YFWLNSLKEFSHAEQCLTG.LQEENYSSALSCIAESL.FYHK.IASL.AASTPLNPLSFQCE.VKLRIDL
RetrocopyYFWLNSLKEFSHAEQCLTG<LQEENYSSALSCIAESLIFYHKRIASL-AASTPLNPLSFQCELVKLRIDL
ParentalLQAFSQLICTCNSLKTS-PPPAIATTIAMTLGNDLQRCGRISNQMKQSMEEFRSLASRYGDLYQASFDAD
LQ.FSQLICTCNSLKTS.PPPAIATTIAMTLGNDL.RCGRIS.QMKQS.EEFRSLAS.YGDLYQASFDAD
RetrocopyLQDFSQLICTCNSLKTS<PPPAIATTIAMTLGNDLERCGRISSQMKQSVEEFRSLASPYGDLYQASFDAD
ParentalSATLRNVELQQQSCLLI
SATLRNVELQQQSCLL.
RetrocopySATLRNVELQQQSCLLM

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 .11 RPM 20 .68 RPM
SRP051959_heart 0 .65 RPM 13 .47 RPM
SRP051959_kidney 0 .11 RPM 19 .08 RPM
SRP051959_liver 0 .13 RPM 19 .75 RPM
SRP051959_lung 0 .47 RPM 16 .54 RPM
SRP051959_lymph_node 0 .18 RPM 20 .80 RPM
SRP051959_skeletal_muscle 0 .11 RPM 8 .80 RPM
SRP051959_spleen 0 .38 RPM 21 .26 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_1798 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1798 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1798 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 ENSCJAG00000015814 1 retrocopy
retro_cjac_1798 ,


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