RetrogeneDB ID:

retro_cjac_1490

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:16:95220112..95221576(+)
Located in intron of:ENSCJAG00000015651
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MSL3
Ensembl ID:ENSCJAG00000001061
Aliases:None
Description:male-specific lethal 3 homolog (Drosophila) [Source:HGNC Symbol;Acc:7370]


Retrocopy-Parental alignment summary:






>retro_cjac_1490
TCCTGTGTGGCCCAGTGCCACATGAGCTATGGTGGGACGCCTGGAGGTTCAACCCAGATTGCTGATGTTATTGGTGGGAA
AGATGAGAGAGGCAGAAAGATCCCAGAATATCTAATCCATTTTAATAGCTGGAACAGAAGCTGTGATAGATGGGCAGCCA
AACATCATGCGGACTATGATACAGGTGCAAATCACGGATGACGGCATAAATTGGCAAGAAAAGCTGAAGCTCACCTGAGA
AGCACAGTAAGAAAGAAGTGCTGCAGGCTGTCCGGCATCAACTGTCTAAAAAAGCCTCCCAGTTGAAAGACAAAGTTGAA
AATGCTGAAATTCAATAAGCAGTTCTCCAGCAGTAGTGAAAACAATGATAAAAAATAAAGTGTTACTAAAGAAGAGACTG
AAGTGAAAGAACTAGAGCTGTAAACGAAAAGGGAAATGGAAGAAATAATAACTATAGAAATCCCTGAAGTTCTCATCAAG
CAGCTTGAGGGTGATCACTACTACATTAACAGGAGGAAACAGTTAATGAAACTTCCATGACAAACCAACACTGTAATGAT
TTTGGAGTCCTACCAGAAGGATTTTGCTATCAACAAAGCTTTTTCAGCCAGTGAGAGGCCTTGCCACCATCATACTATGC
GGCACGCCAACAAAACGGTGCATTATATCCCAGCAGAAAAGAATGCTGACCTTCGTAAGGAGATGGTGGATGGGTTAAGA
ATAACCTTTGATTACATTCCCCCATCAGTTTTAATCTATCCATGGGAATAAGCTCAAGATAAAAGGTGACTTCATCTGTT
CTTTCAATTAAGGAAAGCACCACAGACACTAAAAGAAGCCACGGGGAGCTCTGTCCCAGCCCACCTTTGTTGAATCCATC
CATACCACAGTCCACAGAGTGTGAGACAGCCACAGCTGAACTGGCCACGCACAAAAGGCGCAAAGCCAAGCCGGAAACAT
TGCCGGCTCTGAGGCAGTCCATGTGTCACGCCACCAACTGCAAGAGGCTGGCTGGTAACAGGCATCACTTCGCCCAAGTG
CTAGCAGGAGGCCACATCAACCAGCATGCGCACGCTGCTCCTGCACCTGGAGAGGAAAACACCTGTGCATCATCTTCAAT
TACTCCTCTGCCTCCTAGCAAGGAAGAAAGTGCTGCATTTACTGGCTTTAAAGGGAAAAGAACTAATGAAATAAATGAGG
TACTCTTGTGGAAGCTTGTGCCTGATAATTACCCCTCAGGCAACCAGCCACTTCCATCCTCTTCACATTTACAGGGCACA
TTTGCTCTGACTGTTGGTAAAACTTCCAGAAATCCTTGGAAAGATGTCCTAATCTGAGAAGAATCTGAAGGCTTTATTGA
AACACTCTGATCACTTTCTCCAGTTTTTAGCAGAATACCATGATGACTTCTTCCCAGAGTAGGCTTATGTTGCTGCCTGT
GAGGCATATTACAGCAGCTAGAAC

ORF - retro_cjac_1490 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.23 %
Parental protein coverage: 98.62 %
Number of stop codons detected: 10
Number of frameshifts detected 8


Retrocopy - Parental Gene Alignment:

ParentalSCAASAGWAPVGCPGRPIQIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRK
SC.A.......G.PG...QI.DVI.GKDE.GRKIPEYLIHFN.WNRS.DRWAA..H...DT..N.....K
RetrocopySCVAQCHMSYGGTPGGSTQIADVIGGKDERGRKIPEYLIHFNSWNRSCDRWAAKHHADYDTGANHG*RHK
ParentalLARKAVARLRSTGRKKKRCRLPGVDSV-LKGLPSEEKDENDE-NSLNSS-SDSAEDKDEEISEESDIEEK
LARKA.A.LRST.R.KK.CRL.G......K......K.EN.E.NS..SS.S.S.E..D...S......E.
RetrocopyLARKAEAHLRSTVR-KKCCRLSGINCL<KKASQLKDKVENAE<NSISSS<SSSSENNDKK*SV---TKEE
ParentalTEVKQEPELQTKREMEERTITIEIPEVLKKQLEDDCYYINRRKRLVKLPCQTNIITILESYVKHFAINAA
TEVK.E.EL.TKREMEE..ITIEIPEVL.KQLE.D.YYINRRK.L.KLP.QTN...ILESY.K.FAIN.A
RetrocopyTEVK-ELEL*TKREMEE-IITIEIPEVLIKQLEGDHYYINRRKQLMKLP*QTNTVMILESYQKDFAINKA
ParentalFSANERPRHHHVMPHANMNVHYIPAERNVDLCKEMVDGLRITFDYTLPLVLLYPYEQAQYK-KVTSSKFF
FSA.ERP.HHH.M.HAN..VHYIPAE.N.DL.KEMVDGLRITFDY..P.VL.YP.E.AQ.K.KVTSS...
RetrocopyFSASERPCHHHTMRHANKTVHYIPAEKNADLRKEMVDGLRITFDYIPPSVLIYPWE*AQDK<KVTSS--V
ParentalLPIKESATSTARSQEELSPSPPLLNPSTPQSTESQPTTGEPATPKRRKAEPEALQSLRRSTRHTTNCDRL
L.IKES.T.T.RS..EL.PSPPLLNPS.PQSTE....T.E.AT.KRRKA.PE.L..LR.S..H.TNC.RL
RetrocopyLSIKESTTDTKRSHGELCPSPPLLNPSIPQSTECETATAELATHKRRKAKPETLPALRQSMCHATNCKRL
ParentalSES-SASPQP-KRRQQDTSASMPKLFLHLEKKTPVH-SRSSSPIPLTPSKEGSAVFAGFEGRRTNEINEV
.....AS..P.K..Q..TS.SM..L.LHLE.KTPVH.S.S..P.P..PSKE.SA.F.GF.G.RTNEINEV
RetrocopyAGN<QASLRP<KC*QEATSTSMRTLLLHLERKTPVH<SSSITPLP--PSKEESAAFTGFKGKRTNEINEV
ParentalLSWKLVPDHYPPGDQPPP-PSYIYGAQHLLRLFVKLPEILGKMSFSEKNLKALLKHFDLFLRFLAEYHDD
L.WKLVPD.YP.G.QP.P.P..IY.A.HLL.L.VKLPEILGKMS.SEKNLKALLKH.D.FL.FLAEYHDD
RetrocopyLLWKLVPDNYPSGNQPLP>PLHIYRA-HLL*LLVKLPEILGKMS*SEKNLKALLKHSDHFLQFLAEYHDD
ParentalFFPESAYVAACEAHYSTKN
FFPE.AYVAACEA.YS..N
RetrocopyFFPE*AYVAACEAYYSS*N

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 2 .73 RPM 5 .30 RPM
SRP051959_heart 1 .72 RPM 7 .23 RPM
SRP051959_kidney 2 .62 RPM 11 .85 RPM
SRP051959_liver 1 .52 RPM 4 .61 RPM
SRP051959_lung 2 .77 RPM 12 .30 RPM
SRP051959_lymph_node 3 .86 RPM 9 .06 RPM
SRP051959_skeletal_muscle 1 .09 RPM 5 .33 RPM
SRP051959_spleen 3 .66 RPM 9 .79 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_1490 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1490 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1490 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4097
Pan troglodytes retro_ptro_2778
Gorilla gorilla retro_ggor_2749
Parental genes homology:
Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000092781 retrocopy
retro_btau_883,
Callithrix jacchus ENSCJAG00000001061 1 retrocopy
retro_cjac_1490 ,
Cavia porcellus ENSCPOG000000046925 retrocopies
retro_cpor_1423, retro_cpor_1424, retro_cpor_1425, retro_cpor_1426, retro_cpor_95,
Homo sapiens ENSG000000053022 retrocopies
retro_hsap_2401, retro_hsap_4097,
Gorilla gorilla ENSGGOG000000065822 retrocopies
retro_ggor_1820, retro_ggor_2749,
Macaca mulatta ENSMMUG000000026892 retrocopies
retro_mmul_2362, retro_mmul_972,
Monodelphis domestica ENSMODG000000173501 retrocopy
retro_mdom_1422,
Pongo abelii ENSPPYG000000201232 retrocopies
retro_pabe_2166, retro_pabe_3353,
Pan troglodytes ENSPTRG000000216622 retrocopies
retro_ptro_1751, retro_ptro_2778,
Pteropus vampyrus ENSPVAG000000050001 retrocopy
retro_pvam_203,
Sorex araneus ENSSARG000000084771 retrocopy
retro_sara_139,
Tarsius syrichta ENSTSYG000000127884 retrocopies
retro_tsyr_1079, retro_tsyr_1649, retro_tsyr_1706, retro_tsyr_948,


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