RetrogeneDB ID: | retro_cjac_397 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:56885310..56886701(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MEN1 | ||
| Ensembl ID: | ENSCJAG00000002716 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_397
GGCACCAAATTTGACAGCTCTGATGTGGCCTTTGCTGTGGTTGGGGTTTGCCAGGCCTTGGGTGTCTGGGATGTCCTCCT
CGCCCTGTCTGAGGATCATGCCTGGGTAGTGTTTGGACCCAATGGGGAGCAGACAGCTGAGGTCACCTAGCATGGCAAGG
GCATTAAGAACTGCAGGTGCCAGACGGTCAACACTGGTGTGGCTAAGCGGAGCTGGCTGTACCTGAAAGGATCATACATG
CGCTGTGACCGCAAGGTGGAGATGGCGTTCATGGTGTGTGCCATCAGCTCTTCCATTGACCTATATACTGACTCATTAGA
GCTGCTGCAGGTACAGCAGAAGCTGCTCTGGCTGCTCTATGACCTGGGACATCTGGAAAGGTACCCCATGGCCTTAGGGA
ACTTGGAAGATCTAGAGGATCTGGAGCCTACTCCTGGCCAGCCAGACCCACTCACCTTCTACCACAAGGGCATTGCCTCA
GCTAAAACCTATCAGGATGAACACATCTACCCCTGCATGTACGTGGCTGGCTAACACTGTCACAACCAAAATGTGTGTGA
AGCCCTGCAGGCCTGGGCTGACACGGCCACTGTCATGCAGGACTACAACTACTGCCGGGAAGACGAGGAGATCCACAAGG
AGTTCTTTGAAGTAGCCAATGATGTCATCCCCAGCCTGCTGAAGGAGGCAGCCAGCTTGCTAGAGGTGGACATGGAGCCG
TCGCGGGGAGCAGAGCCAGGGCACCCAGAGCCAAGATTCTGTCTCCAGGACCCTGAGTGCTTTGCCCACCTGCTGCGATT
CTGTGGCAGGATCTGCAAATGGGAGGAGGGCAGTCCCACGCCTGTGTTGCATGTGGGCTGGGCCACCTTCCTTGTGCAGT
CCCTAGGCTGTTTCGAGGAACAGGTGCAGCAGAAGGTGAGCATAATGAGCCGGGAGGCCGAGGAGGCTGAGGCAGAGCAG
CTGTGGGTTGAGGAAGCCCAGGAAGGCCGGTGGCAGGCCCCACGGCGGTCGTCCAAGCTAGAGGAGCCCCCGCCCCCCAA
GAAGCCATCACTGGACAAGGGCCCAGGCGCCAGCCAGGGTGCGGTGTCAGGACTTCCCCCACCCCACCCCCAGAAACCCC
TGGGACAGTCCCTGGCACAGATCAAGGCCCTGAAGGTGGCAGCACGGCTCAGGCGCCAGCGCCTGCAGCATCACCACTGC
TGGAAGGTCCAGTGCTCACTTTCCAGAACAAGAAGATGAAGGGCATGAAGGAGCTGCTGGTGGCCACCAAGGTCAACTCA
AGCGCCATCAAGCTGCAACTCACGGCGCAGTCCCAAGTTCAGATGAAGAAGCAGAAGGTGTCCACCCCTAGTGAATACAC
TCTGACTTTCCGCAAGTGGCAGCGCAAAGGC
ORF - retro_cjac_397 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.06 % |
| Parental protein coverage: | 99.78 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | GTKLDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAER |
| GTK.DSS.VAFAVVG.CQALG..DV.LALSEDHAWVVFGPNGEQTAEVT.HGKG....R.QTVN.GVA.R | |
| Retrocopy | GTKFDSSDVAFAVVGVCQALGVWDVLLALSEDHAWVVFGPNGEQTAEVT*HGKGIKNCRCQTVNTGVAKR |
| Parental | SWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEE |
| SWLYLKGSYMRCDRK.E.AFMVCAI..SIDL.TDSLELLQ.QQKLLWLLYDLGHLERYPMALGNL.DLE. | |
| Retrocopy | SWLYLKGSYMRCDRKVEMAFMVCAISSSIDLYTDSLELLQVQQKLLWLLYDLGHLERYPMALGNLEDLED |
| Parental | LERTPGRPDPLTLYHKGFPLIWTVYRVKCVEHCGGLAGYHCRNRNVREALQDWADTATVIQDYNYCREDE |
| LE.TPG.PDPLT.YHKG.....T.Y.......C...AG.HC.N.NV.EALQ.WADTATV.QDYNYCREDE | |
| Retrocopy | LEPTPGQPDPLTFYHKGIASAKT-YQDEHIYPCMYVAG*HCHNQNVCEALQAWADTATVMQDYNYCREDE |
| Parental | EIYKEFFEVANDVIPNLLKEAASLLEAGEE-RPGEQSQGTQSQGSA-LQDPECFAHLLRFYDGICKWEEG |
| EI.KEFFEVANDVIP.LLKEAASLLE...E.R.GEQSQGTQSQ.S..LQDPECFAHLLRF...ICKWEEG | |
| Retrocopy | EIHKEFFEVANDVIPSLLKEAASLLEVDME>RRGEQSQGTQSQDSV<LQDPECFAHLLRFCGRICKWEEG |
| Parental | SPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSREAEAAEAEEPWGEEAREGRRRGPRRESKPEEPPPPK |
| SPTPVLHVGWATFLVQSLG.FE.QV.QKV.I.SREAE.AEAE..W.EEA.EGR...PRR.SK.EEPPPPK | |
| Retrocopy | SPTPVLHVGWATFLVQSLGCFEEQVQQKVSIMSREAEEAEAEQLWVEEAQEGRWQAPRRSSKLEEPPPPK |
| Parental | KPALDKG----QGAVSGPP----RKPPG-TVPGTARGPEGGSTAQAPAPAASPPLEGPVLTFQSEKMKGM |
| KP.LDKG....QGAVSG.P.....KP.G.TVPGT..GPEGGSTAQAPAPAASP.LEGPVLTFQ..KMKGM | |
| Retrocopy | KPSLDKGPGASQGAVSGLPPPHPQKPLG<TVPGTDQGPEGGSTAQAPAPAASPLLEGPVLTFQNKKMKGM |
| Parental | KELLVATKINSSAIKLQLTAQSQVQMKKQKVSTPSDYTLSFLKRQRKG |
| KELLVATK.NSSAIKLQLTAQSQVQMKKQKVSTPS.YTL.F.K.QRKG | |
| Retrocopy | KELLVATKVNSSAIKLQLTAQSQVQMKKQKVSTPSEYTLTFRKWQRKG |
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 .00 RPM | 1 .86 RPM |
| SRP051959_heart | 0 .00 RPM | 2 .25 RPM |
| SRP051959_kidney | 0 .02 RPM | 2 .60 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .27 RPM |
| SRP051959_lung | 0 .00 RPM | 2 .93 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 3 .47 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .83 RPM |
| SRP051959_spleen | 0 .00 RPM | 2 .46 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_397 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_397 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_397 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 | ENSCJAG00000002716 | 1 retrocopy |
retro_cjac_397 ,
|