RetrogeneDB ID: | retro_cjac_1764 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:18316903..18317766(+) | ||
| Located in intron of: | ENSCJAG00000018862 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000018920 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MTHFD2L | ||
| Ensembl ID: | ENSCJAG00000013883 | ||
| Aliases: | None | ||
| Description: | Probable bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase 2 NAD-dependent methylenetetrahydrofolate dehydrogenase Methenyltetrahydrofolate cyclohydrolase [Source:UniProtKB/Swiss-Prot;Acc:F6ZFR0] |
Retrocopy-Parental alignment summary:
>retro_cjac_1764
TTCCACCTCGTGGCAGTTCGAAATGAAGCCGTGGTCATTTCTGGAAGGAAACTGACCCAGCAGATCAAGCAGGAAGGGCA
GCAGGAGATGGAAGAGTGGGTGGCCTCAGGCAATAAGTGGCCACAACTTAGCGTGATCCTCTTTGCCGAGCATCCTGCAA
GTCACTGCTATGTCCTCAACAAAACCAGGGCAGCTGCAGGTATGGGAATCAACAGTGAGACAGTTGTGAAACCGGCTCCA
ATTTCAGAGGAAGAATTGTTGAATTTAATGAATAAACTGAATAATGATGATAACGTAGATGGCCTCCTTGTTCAGCCGGC
TCTTCCAGAGCATATTGATGAGAGAAAGATCTGCAATGCCATTTCTCCAGACAAGGACGTTGATGGCTTTCATGTAATTA
ATGTAGGGCGAATGTGTTTGGACCAGTATTCCATGTTACTGGCTACCCCGCGGGGTGTGGGGAAAATAATTAAGCGAACT
GGCATTCCAACCCTAGGGAAGAATGTGGTTGTGGCTGGAAGGTCAAAAAATGTAGGAATGCCCAGTGCAATGTTACTGCA
CACAGGGCACATGAACGTCCCGGAGGTGATGCCACTGTCACAACATCTCATCGATATACTTCCAAAGAACAGTTGAAGAA
ACATATAATTCTTGCAGATATTGTAATATCTGCTGCAGGCATTCCAAATCTGATCACAGCAGATATGATCAAGGAAGGAG
CAGCAGTTATTGATGTGGGAATAAATAGAGTTCACAATCCCATAACTGCCAAACCCAAGTTGGTTGGAGATGTGGATTTT
GAAGGAGTCAGACAAAAAGCCAGTTCTATCACTCCAGTTCCTGGAGGGCTTGTCCCCATGAGT
ORF - retro_cjac_1764 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.41 % |
| Parental protein coverage: | 83.29 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | FRSSGVRHEAVIISGTEMAKHIQKEIKQGVESWISLGNRRPHLSIILVGDNPASHTYVRNKIRAASAVGI |
| F....VR.EAV.ISG......I..E..Q..E.W...GN..P.LS.IL....PASH.YV.NK.RAA...GI | |
| Retrocopy | FHLVAVRNEAVVISGRKLTQQIKQEGQQEMEEWVASGNKWPQLSVILFAEHPASHCYVLNKTRAAAGMGI |
| Parental | CSELILKPKDVSQEELLDITDQLNMDPRVSGILVQLPLPDHVDERMICNGIAPEKDVDGFHIINIGRLCL |
| .SE...KP...S.EELL.....LN.D..V.G.LVQ..LP.H.DER.ICN.I.P.KDVDGFH.IN.GR.CL | |
| Retrocopy | NSETVVKPAPISEEELLNLMNKLNNDDNVDGLLVQPALPEHIDERKICNAISPDKDVDGFHVINVGRMCL |
| Parental | DQHSLIPATASAVWEIITRTGIQTFGKNVVVAGRSKNVGMPIAMLLHTDGEHERP-GGDATVTIAHRYTP |
| DQ.S...AT...V..II.RTGI.T.GKNVVVAGRSKNVGMP.AMLLHT.G....P.GGDATVT..HRYT. | |
| Retrocopy | DQYSMLLATPRGVGKIIKRTGIPTLGKNVVVAGRSKNVGMPSAMLLHT-GHMNVP<GGDATVTTSHRYTS |
| Parental | KEQLKTHTQLADVIIVAAGIPKLITSDMVKEGAAVIDVGINYVHDPVTGKTKLVGDVDFEAVKKKAGFIT |
| KEQLK.H..LAD..I.AAGIP.LIT.DM.KEGAAVIDVGIN.VH.P.T.K.KLVGDVDFE.V..KA..IT | |
| Retrocopy | KEQLKKHIILADIVISAAGIPNLITADMIKEGAAVIDVGINRVHNPITAKPKLVGDVDFEGVRQKASSIT |
| Parental | PVPGGVGPMT |
| PVPGG..PM. | |
| Retrocopy | PVPGGLVPMS |
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 | 1 .80 RPM |
| SRP051959_heart | 1 .53 RPM | 1 .28 RPM |
| SRP051959_kidney | 2 .09 RPM | 1 .66 RPM |
| SRP051959_liver | 0 .15 RPM | 28 .94 RPM |
| SRP051959_lung | 1 .17 RPM | 4 .15 RPM |
| SRP051959_lymph_node | 3 .40 RPM | 0 .39 RPM |
| SRP051959_skeletal_muscle | 0 .96 RPM | 2 .29 RPM |
| SRP051959_spleen | 1 .13 RPM | 1 .07 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1764 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1764 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1764 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 10 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000006627 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000013883 | 1 retrocopy |
retro_cjac_1764 ,
|
| Callithrix jacchus | ENSCJAG00000017810 | 3 retrocopies | |
| Tupaia belangeri | ENSTBEG00000009980 | 4 retrocopies | |
| Tursiops truncatus | ENSTTRG00000002366 | 1 retrocopy |