RetrogeneDB ID: | retro_ecab_862 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 5:69095771..69097401(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PAPSS1 | ||
| Ensembl ID: | ENSECAG00000021678 | ||
| Aliases: | None | ||
| Description: | 3'-phosphoadenosine 5'-phosphosulfate synthase 1 [Source:HGNC Symbol;Acc:8603] |
Retrocopy-Parental alignment summary:
>retro_ecab_862
ATGGTTTGCCTTGCTATTCCATGCTGCACTTTGGATGGTGACAACATTCATCAAGGTCTCAATAAAAATCTTGGCTTTAG
TCCTGAAGACAGAGAAGAGAATTTCAATGCATTACAGGGGTTGCTAAACTATTTGCAGATGTGGGCTTAGTGTGCATCGC
AAGTTTTATATCGCTTTATACTCAGGATCACAGCAATGCAAGGCAAATTCATGAGGGTGCAAATTTACCTTTTTCTAAAC
TATTTGTTGATGCTCCTAAGCATGTTTGTGGACAGAGAGATGTCAAAGAACTCTACAGACAAGCATGGGCTGGAGAAATT
AAAGATTTCACTGGGATTGATTCTGAATGTGAAAAACCAAGACCCCTGAATTAGTGTTGAAAATAGACTCCTGTGATATA
AATGACTGCATCCAGCAAATTGTGAAACTTCTACAGGAATGGGATATCATACTCATGAATACCTCTTATGAAGTAAAAGA
ACTGTATGTGCCAGAAAATAAACTACATTTGTCAAAAACAGATGCAGAAACATTACTGGCACTGAAAATTAGTAAGTGGA
TATGCAGTGGGTACAGATTTTGTGGAAGGTTGGGAAACCCCACTGAATGACTTTATGAGAGAGAAAGAGTACTTACAATG
CCATCATTTCGATTGTCTTCTGGATGGGGGTGTCATGAACTTGCCAGTGCCTATAGTTCTGATAGCTATTCATGAAGATA
AAGAGAGGCTAGATGGTCAAACAGCATTTGCTCTGATGTAGGAGGGCTGCTATCTGGCTATTTTTCACAGTTCAAAGTTC
TTTGAGCACAGGATGGAAGAGTGCTGTGCCAGACAGTGGGGAACAACGTGCAAGAACCAACCCTACATCAAGATGGTTAT
GGAACAAGGAGGTTGGCTGATTGGAAGAGATCTTCAAGTCTGGGACCAAGTTCATTGGAATGATGGTCTTGGTTAGTATT
GTTTTACTCCGCCCGAGCTAAAGCAGATGTTTAAAGGTATGAATGCTGATGCTATCTTTGCATTTCAATTACATAAGCCA
TTGCTCAACAGACATGCTCTATTAATGCAGGATACCCATTAGCAATTTCTAGAGAGGGGCTACTGGCACCTTGTCCTTTT
CAATCACTTTCTTGATGGCTAGACAAAGGATGATGATGTTCCTTTGGTGTAGTTCTTGAAGCAGCATGCTGCAGTGCTGA
AGGGAGGAGTTCTGAATCCTGAAACAACAGTGATGCCATTTTCCTATCTCCCATGGTGTATGCTGGATCACCTGATGTCC
AGTGGCATTGCAGAGCACGGATGGTTGCAGGAATCAATTTTTACATTATAGGGTGAGACCCTGAGGGTGTGCCTCGTCCA
GAAGCAGGGAAGGATCTTTATGAACCAATTCATGACACCAAAGTGCCGACAATTGCCCCTGGCCTAATCATCTTGGAAAT
GATTGCAACTTAAAACAAGCAAAAGAAGCATATGGACTACTATGACTCTGAACACCATGAAGACTTTGAATTTATTTCAA
GAACACATATGTGCAAACTTAGCTGAGAAGGCCAGAAGTTTCCTGAAGTTTTTGTGACTCCCAAGGCCTAGGCTGTGCTG
ATGGAATACTAGAAATACTTGGAGAAAGCT
ORF - retro_ecab_862 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.1 % |
| Parental protein coverage: | 90.89 % |
| Number of stop codons detected: | 10 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | LVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRR-IAEVAKLFADAGLVCITSFISPYTQDRNNARQ |
| .VC..IPC.TLDGDNI.QGLNKNLGFSPEDREEN....I..VAKLFAD.GLVCI.SFIS.YTQD..NARQ | |
| Retrocopy | MVCLAIPCCTLDGDNIHQGLNKNLGFSPEDREENFNA<ITGVAKLFADVGLVCIASFISLYTQDHSNARQ |
| Parental | IHEGASLPFFEVFVDAPLHVCEQRDVKGLYKKARAGEIKGFTGIDSEYEKP-EAPELVLKTDSCDVNDCV |
| IHEGA.LPF...FVDAP.HVC.QRDVK.LY..A.AGEIK.FTGIDSE.EKP...PELVLK.DSCD.NDC. | |
| Retrocopy | IHEGANLPFSKLFVDAPKHVCGQRDVKELYRQAWAGEIKDFTGIDSECEKP<KTPELVLKIDSCDINDCI |
| Parental | QQVVELLQERDIVPVDASYEVKELYVPENKLHLAKTDAETLPALKINK-VDMQWVQVL-AEGWATPLNGF |
| QQ.V.LLQE.DI.....SYEVKELYVPENKLHL.KTDAETL.ALKI.K.VDMQWVQ.L..EGW.TPLN.F | |
| Retrocopy | QQIVKLLQEWDIILMNTSYEVKELYVPENKLHLSKTDAETLLALKISK<VDMQWVQIL<VEGWETPLNDF |
| Parental | MREREYLQCLHFDCLLDGGVINLSVPIVLTATHEDKERLDGCTAFALMYEGRRVAILRNPEFFEHRKEER |
| MRE.EYLQC.HFDCLLDGGV.NL.VPIVL.A.HEDKERLDG.TAFALM.EG...AI.....FFEHR.EE. | |
| Retrocopy | MREKEYLQCHHFDCLLDGGVMNLPVPIVLIAIHEDKERLDGQTAFALM*EGCYLAIFHSSKFFEHRMEEC |
| Parental | CARQWGTTCKNHPYIKMVMEQGDWLIGGDLQVLDRIYWNDGLDQYRFTPTELKQKFKDMNADAVFAFQLR |
| CARQWGTTCKN.PYIKMVMEQG.WLIG.DLQV.D...WNDGL..Y.FTP.ELKQ.FK.MNADA.FAFQL. | |
| Retrocopy | CARQWGTTCKNQPYIKMVMEQGGWLIGRDLQVWDQVHWNDGLG*YCFTPPELKQMFKGMNADAIFAFQLH |
| Parental | NPVHNGHALLMQDTHQQLLERGYRRPVLLLHPLGGWTKDDDVPLMWRMKQHAAVLDEGVLNPATTVV-AI |
| .P..N.HALLMQDTH.Q.LERGY...VL..H.L.G.TKDDDVPL....KQHAAVL..GVLNP.TTV..AI | |
| Retrocopy | KPLLNRHALLMQDTH*QFLERGYWHLVLFNHFLDG*TKDDDVPLV*FLKQHAAVLKGGVLNPETTVM<AI |
| Parental | FPSPMMYAGPTEVQWHCRARMVAGANFYIVGRDPAGLPHPETGKDLYEPTHGAKVLTMAPGLITLEIVPF |
| F.SPM.YAG...VQWHCRARMVAG.NFYI.G.DP.G.P.PE.GKDLYEP.H..KV.T.APGLI.LE.... | |
| Retrocopy | FLSPMVYAGSPDVQWHCRARMVAGINFYIIG*DPEGVPRPEAGKDLYEPIHDTKVPTIAPGLIILEMI-- |
| Parental | RVAAYNKKKKQMDYYDSEHNEDFEFISGTRMRKLAREGQKPPEGFMAPKAWTVLMEYYKSLEKA |
| ..A..NK.KK.MDYYDSEH.EDFEFIS.T.M.KL..EGQK.PE.F..PKA..VLMEY.K.LEKA | |
| Retrocopy | --AT*NKQKKHMDYYDSEHHEDFEFISRTHMCKLS*EGQKFPEVFVTPKA*AVLMEY*KYLEKA |
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 |
|---|---|---|
| SRP021940_articular_cartilage | 0 .06 RPM | 177 .68 RPM |
| SRP021940_cerebellum | 0 .05 RPM | 157 .77 RPM |
| SRP021940_embryo | 0 .03 RPM | 152 .16 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 92 .04 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 100 .69 RPM |
| SRP021940_testis | 0 .00 RPM | 33 .51 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_862 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_862 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_862 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 | ENSCJAG00000015905 | 1 retrocopy | |
| Equus caballus | ENSECAG00000021678 | 1 retrocopy |
retro_ecab_862 ,
|