RetrogeneDB ID: | retro_cjac_308 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 11:103313552..103315475(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000011116 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LRRC4B | ||
| Ensembl ID: | ENSCJAG00000017224 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_308
ATGTTGAACAAGATGACCTTACATCCACAGCAGATAATGATAGGTCCTAGGTTTAACAGGGCCCTATTTGACCCCCTGCT
TGTGGCGCTGCTGGCTCTTCAACTTCTTGTGGTGGCTGGTCTGGTGCGGGCTCAGACCTGCCCTTCTGTGTGCTCCTGCA
GCAACCAATTCAGCAAGGTGATTTGCGTTCGGAAAAACCTGCGTGAGGTTCCGGATGGCATCTCCACCAACACACGGCTG
CTGAACCTCCATGAGAACCAAATCCAGATCATCAAAGTGAACAGCTTCAAGCACTTGAGGCACTTGGAAATCCTACAGTT
GAGTAGGAACCATATCAGAACCATTGAAATTGGGGCTTTCAATGGTCTGGCGAACCTCAATACTCTGGAACTTTTTGACA
ATCGTCTTACTACCATCCCGAATGGAGCTTTTGTATACTTATCTAAACTGAAGGAGCTCTGGTTGCGAAACAACCCCATT
GAAAGCATCCCTTCTTATGCTTTTAACAGAATTCCTTCTTTGCGCCGACTAGACTTAGGGGAATTGAAAAGACTTTCATA
CATCTCAGAAGGTGCCTTTGAAGGTCTGTCCAACTTGAGGTATTTGAACCTTGCCATGTGCAACCTTCGGGAAATACCTA
ACCTCACGCCGCTCATAAAACTAGATGAGCTGGATCTTTCTGGGAATCATTTATCTGCCATCAGGCCTGGCTCTTTCCAG
GGTTTGATGCACCTTCAAAAACTGTGGATGATACAGTCCCAGATTCAAGTGATTGAACGGAATGCCTTTGACAACCTTCA
GTCACTAGTGGAGATCAACCTGGCACACAATAATCTAACATTATTGCCTCATGACCTCTTCACTCCCTTGCATCATCTAG
AGCGGATACATCTACATCACAACCCTTGGAACTGTAACTGTGACATACTGTGGCTCAGCTGGTGGATAAAAGACATGGCC
CCCTCCAACACAGCTTGTTGTGCCCGGTGTAACACTCCTCCCAATCTAAAGGGGAGGTACATTGGAGAGCTCGACCAGAA
TTATTTCACATGCTATGCTCCAGTGATTGTGGAGCCCCCTGCAGACCTCAATGTCACTGAAGGCATGGCAGCTGAGTTGA
AATGTCGGGCCTCCACCTCCCTGACATCTGTATCTTGGATTACTCCAAATGGAACAGTCATGACACATGGGGCATACAAA
GTGAGGATAGCTGTGCTCAGTGATGGTACGTTAAATTTCACAAATGTAACTGTGCAAGATACAGGCATGTACACATGTAT
GGTGAGTAATTCCGTTGGGAATACTACCGCTTCAGCCACCCTGAATGTTACTGCGGCAACCACTACTCCTTTCTCTTACT
TTTCAACTGTCACAGTAGAGACTATGGAACCGTCTCAGGATGAGGCACGGACCACAGATAACAATGTGGGTCCCACTCCA
GTGGTTGACTGGGAGACCACCAATGTGACCACCTCTCTCATGCCACAGAGCACAAGGTCAACAGAGAAAACCTTCACCAT
CCCAGTGACTGATATAAACAGTGGGATCCCAGGAATCGATGAGGTCATGAAGACTACCAAAATTATCATTGGGTGTTTTG
TGGCCATCACACTCATGGCTGCAGTGATGCTGGTCATTTTCTACAAGATGAGGAAGCAGCACCATCGGCAAAACCATCAT
GCCCCAACAAGGACTGTTGAAATCATTAATGTGGATGATGAGATTACGGGAGACACACCCATGGAAAGCCACCTGCCCAT
GCCTGCTATCGAGCATGAGCACCTAAATCACTATAACTCATACAAATCTCCCTTCAACCACACAACAACAGTTAACACAA
TAAATTCAATACACAGTTCAGTGCATGAACCGTTATTGATCCGAATGAACTCTAAAGACAATGTACAAGAGACTCAAATC
TAA
ORF - retro_cjac_308 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.8 % |
| Parental protein coverage: | 80.89 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VAVTSAAAGGSPPATSCPEACSCSNQASRVICTRRELAEVPASIPVNTRYLNLQENGIQVIRTDTFKHLR |
| .A.......G...A..CP..CSCSNQ.S.VIC.R..L.EVP..I..NTR.LNL.EN.IQ.I....FKHLR | |
| Retrocopy | LALQLLVVAGLVRAQTCPSVCSCSNQFSKVICVRKNLREVPDGISTNTRLLNLHENQIQIIKVNSFKHLR |
| Parental | HLEILQLSKNLVRKIEVGAFNGLPSLNTLELFDNRLTTVPTQAFEYLSKLRELWLRNNPIESIPSYAFNR |
| HLEILQLS.N..R.IE.GAFNGL..LNTLELFDNRLTT.P..AF.YLSKL.ELWLRNNPIESIPSYAFNR | |
| Retrocopy | HLEILQLSRNHIRTIEIGAFNGLANLNTLELFDNRLTTIPNGAFVYLSKLKELWLRNNPIESIPSYAFNR |
| Parental | VPSLRRLDLGELKRLEYISEAAFEGLVNLRYLNLGMCNLKDIPNLTALVRLEELELSGNRLDLIRPGSFQ |
| .PSLRRLDLGELKRL.YISE.AFEGL.NLRYLNL.MCNL..IPNLT.L..L.EL.LSGN.L..IRPGSFQ | |
| Retrocopy | IPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMCNLREIPNLTPLIKLDELDLSGNHLSAIRPGSFQ |
| Parental | GLTSLRKLWLMHAQVATIERNAFDDLKSLEELNLSHNNLMSLPHDLFTPLHRLERVHLNHNPWHCNCDVL |
| GL..L.KLW....Q...IERNAFD.L.SL.E.NL.HNNL..LPHDLFTPLH.LER.HL.HNPW.CNCD.L | |
| Retrocopy | GLMHLQKLWMIQSQIQVIERNAFDNLQSLVEINLAHNNLTLLPHDLFTPLHHLERIHLHHNPWNCNCDIL |
| Parental | WLSWWLKETVPSNTTCCARCHAPAGLKGRYIGELDQSHFTCYAPVIVEPPTDLNVTEGMAAELKCRTGTS |
| WLSWW.K...PSNT.CCARC..P..LKGRYIGELDQ..FTCYAPVIVEPP.DLNVTEGMAAELKCR..TS | |
| Retrocopy | WLSWWIKDMAPSNTACCARCNTPPNLKGRYIGELDQNYFTCYAPVIVEPPADLNVTEGMAAELKCRASTS |
| Parental | MTSVNWLTPNGTLMTHGSYRVRISVLHDGTLNFTNVTVQDTGQYTCMVTNSAGNTTASATLNVSA--VDP |
| .TSV.W.TPNGT.MTHG.Y.VRI.VL.DGTLNFTNVTVQDTG.YTCMV.NS.GNTTASATLNV.A....P | |
| Retrocopy | LTSVSWITPNGTVMTHGAYKVRIAVLSDGTLNFTNVTVQDTGMYTCMVSNSVGNTTASATLNVTAATTTP |
| Parental | NTYFTTVTVETLETQPGEEALQPRGTEKEPPGPTTDGVSSSTTAPAPRSSRPTEKAFTVPITDVTENALK |
| ..YF.TVTVET.E..P.............P...........TT...P.S.R.TEK.FT.P.TD....... | |
| Retrocopy | FSYFSTVTVETME--PSQDEARTTDNNVGPTPVVDWETTNVTTSLMPQSTRSTEKTFTIPVTDI-NSGIP |
| Parental | DLDDVMKTTKIIIGCFVAITFMAAVMLVAFYKLRKQHQLHKHHGPTRTVEIINVEDEL |
| ..D.VMKTTKIIIGCFVAIT.MAAVMLV.FYK.RKQH....HH.PTRTVEIINV.DE. | |
| Retrocopy | GIDEVMKTTKIIIGCFVAITLMAAVMLVIFYKMRKQHHRQNHHAPTRTVEIINVDDEI |
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 | 0 .07 RPM |
| SRP051959_heart | 0 .58 RPM | 0 .11 RPM |
| SRP051959_kidney | 0 .82 RPM | 0 .04 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .02 RPM |
| SRP051959_lung | 0 .08 RPM | 0 .02 RPM |
| SRP051959_lymph_node | 0 .09 RPM | 0 .00 RPM |
| SRP051959_skeletal_muscle | 0 .13 RPM | 0 .00 RPM |
| SRP051959_spleen | 0 .15 RPM | 0 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_308 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_308 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_308 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 | ENSCJAG00000017224 | 1 retrocopy |
retro_cjac_308 ,
|
| Otolemur garnettii | ENSOGAG00000002426 | 1 retrocopy |