RetrogeneDB ID: | retro_cjac_3885 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL285806.1:20751..22658(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000000717 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | POLR3E | ||
| Ensembl ID: | ENSCJAG00000008918 | ||
| Aliases: | None | ||
| Description: | polymerase (RNA) III (DNA directed) polypeptide E (80kD) [Source:HGNC Symbol;Acc:30347] |
Retrocopy-Parental alignment summary:
>retro_cjac_3885
AGAAGCAAAGGGGAGCAGATTGAGCTGAACGTGGACGGGGCCTGCGTGGATGAGACCAGCACGTACTCCTCGAAGCTGAT
GGACAAGCAGACCTTCTGCTCTTCCCAGACCACCAGGAACACATCCCATTACGCCGCTGCACTCTACAGGCAAGGTGAGC
TCTACCTGACACCTTCACATGGCATTTTGCAGCTGCGGCCCAGCTTCTCCTACCTGGATAAGGCGGACGCCAAGCACCGG
GAGAGGGAGGCAGGCGATGAAGCAGGGGACTCTTCACAGGATGAGGTGGAAGACGATGTTAAGCAGATCACGGTGGGGTC
CTCGCGGCCCGAGTCACGCAGGCCCCCGCGCCGCTTGTCCTATGAGTTCCTGCAGAAGAAGCATGCGCAGGAGGCCTGGG
TCCACCTGCATTACTATGGCCTGAAGGACAGCCGCTCTGAGCACGAGCGCCAGTACCTGCTATGCCCAGGCTCGAGCGGG
GAGGAGAACACAGAGCTTGTCAAGTCACCCAGTGAGTACCTGTTGATGCTGATGCCGCCCAGCCAGGAGGAGGAGAAAGA
CAAGCCTGTGGCCTCCAGCAACGTCCTGTCCATGGCCCCGCTGCGCACGCTGCCCCTGGCCGGTCAGATCAAGATCCTGA
TGAAGAACGTGAAGGCCATGCCTTTGGCCAACTTGATGAGCCTCCTGGGCCCCGCCATCGATTCCGTGGCTGTTCTGCGC
GGCATCCAGAAGGTGGCGATGTTGGTCCAAGGGAGCCCGGTGGTGAAGCGTGACATCCTGTGCTCCAAGGACTTATCCAG
CCGTCACAGCGGCGTGCCCGTGCCCGCCGGAGTGCTCTGCGGCGGCTGAGACTTCGTTATGCGGAAGTTCACGCAGAGCC
GCTGGGTGGTTAGGAACGAGGTGGCAACAGTGACCAAACTCTGCACCGGGGACGTGAAGGACTTCCTGGAGCACGTGGCC
GTGGTGAGGATCAACAACGGCTGGGAGTTCATTCTGCCTTAGGACGGGGAGTTCATCAGAAAGCACCGGGATGCGGTCCA
GCGGCAGCACCTGCTGTGGACGGGTATCCGGGCCACACTGGAAAAAGTCTATAATCCTGTAAAGGAAACCAGGCCAAAGA
AGCCGGATGCACAATCAGGGCCTGCCGGGCTGGTCTCTGGGGACCAGCGGATCCAAGTAGCCAAAACCAAGGCCCGGCAG
AACCACGCGTTGCTGGAGCGGGAACTGCAGCGGCGGAAGGAGCAGCTGCGGGCGCCTGTGGTCCAGCCGGGTGTGCGGAT
CAAGGAGGAGCCAGTGAGGGGGGAGGGCGAGGACGATGACGAGGAGGAGGAGCCCGTGGACACTTGCCCCAGCGGCGGCC
TCCACAGCAGGCTGACCAACGGGCTGCCTCCCGGGCGGGCTTCGGGCACGGACAGCTTCAACGGGCATCCGCCCTCGGGC
TGTGCTAGCACCCCCGTGACCGGGGAACTGAGCGCCTTTGGGAAGGCCACCTTTCAGAGACAGTTTGTGTTCACGCTGAG
TGAAATCCAGCTCCTCTTCAACCTGCACATGGCCAGCCTGCCCCCGGCCACAGGCTCTTCAGTGGCAACTTGGACCGCAT
GCTGCGGGACACGGTGTTGGACGCTTGTTGCAGGGAGATACTGGTACCTTTTCCCACGCAGACTGCTGCTACCCCGGATG
AGCAGAAAGTGTTTGCCCTCTGGGAGTCTGGAGGTACGAGCGATCAGCATCGAAGGGTTTTGATTGAAATGTTTTCCAAA
AATTACCGAGTACGCCGAAGCATGATCCAGTCTCGGTTGACTCAAGAGTGTGGAGAAGATCTCAGTAAACAGGAGGTGGA
TAAAGTACTGAAGGCCTGCTGTGTAAGCTATGGTGGCAGGTGGTACCTTCAAGGGACAGTACAGTCT
ORF - retro_cjac_3885 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.75 % |
| Parental protein coverage: | 90.04 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RSKGEQIALNVDGACADETSTYSSKLMDKQTFCSSQTTSNTSRYAAALYRQGELHLTPLHGILQLRPSFS |
| RSKGEQI.LNVDGAC.DETSTYSSKLMDKQTFCSSQTT.NTS.YAAALYRQGEL.LTP.HGILQLRPSFS | |
| Retrocopy | RSKGEQIELNVDGACVDETSTYSSKLMDKQTFCSSQTTRNTSHYAAALYRQGELYLTPSHGILQLRPSFS |
| Parental | YLDKADAKHREREAANEAGDSSQDEAEDDVKQITVRFSRPESEQARQRRVQSYEFLQKKHAEEAWVHLHY |
| YLDKADAKHREREA..EAGDSSQDE.EDDVKQITV..SRPES.....R...SYEFLQKKHA.EAWVHLHY | |
| Retrocopy | YLDKADAKHREREAGDEAGDSSQDEVEDDVKQITVGSSRPESRRPPRRL--SYEFLQKKHAQEAWVHLHY |
| Parental | YGLKDSRSEHERQYLLCPGSSGVENTELVKSPSEYLLMLMPPSQEEEKDKPVAPSNVLSMAQLRTLPLAD |
| YGLKDSRSEHERQYLLCPGSSG.ENTELVKSPSEYLLMLMPPSQEEEKDKPVA.SNVLSMA.LRTLPLA. | |
| Retrocopy | YGLKDSRSEHERQYLLCPGSSGEENTELVKSPSEYLLMLMPPSQEEEKDKPVASSNVLSMAPLRTLPLAG |
| Parental | QIKILMKNVKVMPFANLMSLLGPSIDSVAVLRGIQKVAMLVQGNWVVKSDILYPKDSSSPHSG--VPAEV |
| QIKILMKNVK.MP.ANLMSLLGP.IDSVAVLRGIQKVAMLVQG..VVK.DIL..KD.SS.HSG..VPA.V | |
| Retrocopy | QIKILMKNVKAMPLANLMSLLGPAIDSVAVLRGIQKVAMLVQGSPVVKRDILCSKDLSSRHSGVPVPAGV |
| Parental | LCRGRDFVMWKFTQSRWVVRKEVATVTKLCTEDVKDFLEHMAVVRINKGWEFILPYDGEFIKKHPDVVQR |
| LC.G.DFVM.KFTQSRWVVR.EVATVTKLCT.DVKDFLEH.AVVRIN.GWEFILP.DGEFI.KH.D.VQR | |
| Retrocopy | LCGG*DFVMRKFTQSRWVVRNEVATVTKLCTGDVKDFLEHVAVVRINNGWEFILP*DGEFIRKHRDAVQR |
| Parental | QHMLWTGIQAKLEKI----KETMPKKLDAQSGPAGLVSGDQRIQVAKTKAQQNHALLERELQWRKEQLRA |
| QH.LWTGI.A.LEK.....KET.PKK.DAQSGPAGLVSGDQRIQVAKTKA.QNHALLERELQ.RKEQLRA | |
| Retrocopy | QHLLWTGIRATLEKVYNPVKETRPKKPDAQSGPAGLVSGDQRIQVAKTKARQNHALLERELQRRKEQLRA |
| Parental | PAVPPGVRIKEEPVSEEGEDDDDEEEEPMETSPSGGVHSRLANGLPPGRAAGTDSFNGHLPPGCASTPMA |
| P.V.PGVRIKEEPV..EGE.DDDEEEEP..T.PSGG.HSRL.NGLPPGRA.GTDSFNGH.P.GCASTP.. | |
| Retrocopy | PVVQPGVRIKEEPVRGEGE-DDDEEEEPVDTCPSGGLHSRLTNGLPPGRASGTDSFNGHPPSGCASTPVT |
| Parental | RELRAFVEATFQRQFVLTLSELKRLFNLHLASLP-PGHTLFSGISDRMLQDTVLAAGCKQILVPFPPQTA |
| .EL.AF..ATFQRQFV.TLSE...LFNLH.ASLP.PGH.LFSG..DRML.DTVL.A.C..ILVPFP.QTA | |
| Retrocopy | GELSAFGKATFQRQFVFTLSEIQLLFNLHMASLP<PGHRLFSGNLDRMLRDTVLDACCREILVPFPTQTA |
| Parental | ASPDEQKVFALWESGDMSDQHRQVLLEIFSKNYRVRRNMIQSRLTQECGEDLSKQEVDKVLKDCCVSYGG |
| A.PDEQKVFALWESG..SDQHR.VL.E.FSKNYRVRR.MIQSRLTQECGEDLSKQEVDKVLK.CCVSYGG | |
| Retrocopy | ATPDEQKVFALWESGGTSDQHRRVLIEMFSKNYRVRRSMIQSRLTQECGEDLSKQEVDKVLKACCVSYGG |
| Parental | MWYLKGTVQS |
| .WYL.GTVQS | |
| Retrocopy | RWYLQGTVQS |
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 .02 RPM | 9 .87 RPM |
| SRP051959_heart | 0 .00 RPM | 11 .16 RPM |
| SRP051959_kidney | 0 .00 RPM | 11 .80 RPM |
| SRP051959_liver | 0 .00 RPM | 7 .84 RPM |
| SRP051959_lung | 0 .05 RPM | 13 .40 RPM |
| SRP051959_lymph_node | 0 .05 RPM | 16 .69 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 18 .15 RPM |
| SRP051959_spleen | 0 .02 RPM | 11 .58 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3885 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3885 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3885 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000008918 | 2 retrocopies |
retro_cjac_3734, retro_cjac_3885 ,
|
| Equus caballus | ENSECAG00000015801 | 1 retrocopy |