RetrogeneDB ID: | retro_cjac_3916 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286236.1:41750..43304(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000007968 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TCF25 | ||
| Ensembl ID: | ENSCJAG00000010545 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3916
GTGTCGCGCCGGGCCCTCAGGAGGCTGAGAGGGGAACAGCGCGGCCACGAGCCCCTGGGGCCAGCGCCCTGCAGTTTGAC
CTCCCTGATGACGATGACGTGGAAGAAGGGCCCAAGTGGGAGCTGGGTGGCCGGCACCTCGGGGAGGCAGGGAAGGAGGG
CGTCCGAGTCAACAACCGGTTCCAGCTGATAAACATTGAAGATCTTGAGGGTGACCCTGTGGTGAATGGGGAGAGGTCTG
GCTCTTCGCTCACAGACACTGCGGCACCGGGGAACAAAGGAAGGGCTGCCTGTGAAAACACAGACACCAAGGCGGAGGAG
GCTGGCCAGGACAGTGCCCCCGGAGCGGTCTAATGCAAGTGGCAAACTCCGGAAGAAGAAAAAGAAACAGAAAACTAAGA
AAAGCAGCACGGGAGAAGCACTGGAAAACGGACTAGAAGATATTGATCGCACCCTAGAGAGAACTGAGGACAGCGGTGGT
TTGAACCGTCCTGGCCCAACTCCCCTGAGCTCCAGGAAGCGCGTTCTCTAAGTGGAGCACAGACATTTGAATCCAGACAC
AGAACTGAAAAGGTATTTTGGTGCTCGGCCAGTCCTGGGGGAACAAAGGCCACGGCAGAGACAGCGCGTATACCCCAAGT
GACATGGCTGACGACCCCTAAGAGCACCTGGCCCCGGTACAGCAAACCAGGTCTGTCCATGCGGCTGCTGGAATCGAAAA
AACGCCTGCCCTTGTTTGAGCACAGTGAGGCGTACCAGCAGGCGCAGCACAAGTTCCTGGTGGCCGTGGAGTCCATGGAG
CCCAACAACATCGTGGTTCTGCTCCAGATAAGCCCATATCACGTGGACTCACTCCTGCAGCTCAGCGATGCCTGCCACTT
TCAAGAGGATCAGGAGATGGCTCGAGACCTCATAGAGAGAGCGCTGTACAGTATGGAGTGTGCGTTCCACCCCTTGTTCA
GCCTCACCAGCGGGGCTTGCCGGCTGGATTACCGCAGACCCGAGAACAGGAGCTTCTACCTGGCCCTCTACAAGCAGATG
AGCTTCCTGGAGAAGCGAGGCTGCCCACGCACCGCCCTGGAGTACTGCAAGCTCATCCTGAGTCTCGAGCCGGATGAGGA
CCCCCTCTGCATGCTGCTGCTCATTGACCACCTGGCCTTGCGGCCCGGAACTACGAATACCTTATCCGCCTCTTCAGGAG
TGAGAGGCTCATCGGAACCTGTCGCAGCTCCCAAATTTTGCCTTCTCTGTTCCACTGGCATATTTCCTGCTGAGCCAACA
GACAGACCTCCCTGGGCACGAGCAGAGCTCTGCCAGGGAGAAGGCCTCGCTCTTGATACAGCAGGCGCTCACCATGTTTC
CTGGAGTCCTCCTGCCCCTGCTCGAGTACTGCAGCGTGCGGCCCGATGCCACCGTGTCCACTCATCGCTTCTTTGGACCC
AATGCTGAGATAAGCCAGCCCCCTGCCCTGAGCCAGCTGGTGAGCCTGTATCTCGGGAGGTCACACTTTCTCTGGAAAGA
GCCCGCCACCATGAGCTGGCTGGAGGAGAACATC
ORF - retro_cjac_3916 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.93 % |
| Parental protein coverage: | 77.37 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | MSRRALRRLRGEQRGQEPLGPG-ALQFDLRDDDDAEEEGLKRELGGRRPGEAGKEGVRVNNRFELINIED |
| .SRRALRRLRGEQRG.EPLGP..ALQFDL.DDDD.EE.G.K.ELGGR..GEAGKEGVRVNNRF.LINIED | |
| Retrocopy | VSRRALRRLRGEQRGHEPLGPA<ALQFDLPDDDDVEE-GPKWELGGRHLGEAGKEGVRVNNRFQLINIED |
| Parental | LEDDPVVNGERSGSSLTDTAAPGNKGRAPCGNTDTKAD-GG-VARTAPPEQSNASGKLRKKKKKQKAKKS |
| LE.DPVVNGERSGSSLTDTAAPGNKGRA.C.NTDTKA..GG..ART.PPE.SNASGKLRKKKKKQK.KKS | |
| Retrocopy | LEGDPVVNGERSGSSLTDTAAPGNKGRAACENTDTKAE<GG<LARTVPPERSNASGKLRKKKKKQKTKKS |
| Parental | STGEAVENGLEDIDRILERIEDSSGLNRPGPAPLSSRKHILYVEHRHLNPDTELKRYFGARAVLGEQRPR |
| STGEA.ENGLEDIDR.LER.EDS.GLNRPGP.PLSSRK..L.VEHRHLNPDTELKRYFGAR.VLGEQRPR | |
| Retrocopy | STGEALENGLEDIDRTLERTEDSGGLNRPGPTPLSSRKRVL*VEHRHLNPDTELKRYFGARPVLGEQRPR |
| Parental | QRQRVYPK-CTWLTTPKSTWPRYSKPGLSMRLLESKKGLSLFAFEHSEEYQQAQHKFLVAVESMEPNNIV |
| QRQRVYPK..TWLTTPKSTWPRYSKPGLSMRLLESKK.L.LF..EHSE.YQQAQHKFLVAVESMEPNNIV | |
| Retrocopy | QRQRVYPK<VTWLTTPKSTWPRYSKPGLSMRLLESKKRLPLF--EHSEAYQQAQHKFLVAVESMEPNNIV |
| Parental | VLLQTSPYHVDSLLQLSDACRFQEDQEMARDLIERALYSMECAFHPLFSLTSGACRLDYRRPENRSFYLA |
| VLLQ.SPYHVDSLLQLSDAC.FQEDQEMARDLIERALYSMECAFHPLFSLTSGACRLDYRRPENRSFYLA | |
| Retrocopy | VLLQISPYHVDSLLQLSDACHFQEDQEMARDLIERALYSMECAFHPLFSLTSGACRLDYRRPENRSFYLA |
| Parental | LYKQMSFLEKRGCPRTALEYCKLILSLEPDEDPLCMLLLIDHLALR-ARNYEYLIRLF-QEWEAHRNLSQ |
| LYKQMSFLEKRGCPRTALEYCKLILSLEPDEDPLCMLLLIDHLALR.ARNYEYLIRLF.QE.EAHRNLSQ | |
| Retrocopy | LYKQMSFLEKRGCPRTALEYCKLILSLEPDEDPLCMLLLIDHLALR<ARNYEYLIRLF<QE*EAHRNLSQ |
| Parental | LPNFAFSVPLAYFLLSQQTDLPEHEQSSAREKASLWIQQALTMFPGVLLPLLEYCSVRPDATVSTHPFFG |
| LPNFAFSVPLAYFLLSQQTDLP.HEQSSAREKASL.IQQALTMFPGVLLPLLEYCSVRPDATVSTH.FFG | |
| Retrocopy | LPNFAFSVPLAYFLLSQQTDLPGHEQSSAREKASLLIQQALTMFPGVLLPLLEYCSVRPDATVSTHRFFG |
| Parental | PNAEISQPPALSQLVSLYLGRSHFLWKEPTTMSWLEENV |
| PNAEISQPPALSQLVSLYLGRSHFLWKEP.TMSWLEEN. | |
| Retrocopy | PNAEISQPPALSQLVSLYLGRSHFLWKEPATMSWLEENI |
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 | 2 .09 RPM | 24 .56 RPM |
| SRP051959_heart | 1 .53 RPM | 24 .50 RPM |
| SRP051959_kidney | 1 .04 RPM | 30 .97 RPM |
| SRP051959_liver | 1 .41 RPM | 28 .79 RPM |
| SRP051959_lung | 3 .37 RPM | 24 .99 RPM |
| SRP051959_lymph_node | 5 .11 RPM | 29 .27 RPM |
| SRP051959_skeletal_muscle | 1 .55 RPM | 20 .09 RPM |
| SRP051959_spleen | 1 .45 RPM | 27 .88 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3916 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3916 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3916 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 | ENSCJAG00000010545 | 1 retrocopy |
retro_cjac_3916 ,
|