RetrogeneDB ID: | retro_tsyr_692 | ||
Retrocopy location | Organism: | Tarsier (Tarsius syrichta) | |
| Coordinates: | scaffold_1711:36778..38386(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PCDHGB3 | ||
| Ensembl ID: | ENSTSYG00000004901 | ||
| Aliases: | None | ||
| Description: | protocadherin gamma subfamily B, 3 [Source:HGNC Symbol;Acc:8710] |
Retrocopy-Parental alignment summary:
>retro_tsyr_692
CAGCAGATCCAATACACTATTCCGGAGGAGCTGGCCAAGGGCTCACTGGTGGGGAACCTCGCCAAGGATCTGGGGCTCAG
TGTCCAGGAGTTGCCAGCTCGAAAACTGCGGGTTAGTGCAGAGGATTATTTCAACATTAGTGCGGAGAGTGGGGATTTGT
TAGTAAGCGGAAGGATAGATCGAGAGAAGATCTGCGGCAGGAAATCTGAGTGCGCGCTAGAATTCGAAATGGTGGCTGAA
AATCCAATGAATGTTTTCCACGTGATTGTTGCAATTCAAGATATTAATGACAACGCACCATATTTCGTTGCAAAAGGCAT
CGATTTAGAGATTTGTGAGTCAGCCTTACCAGGGGTGAAATTCCCTCTGGACTCCGCACAAGATGCAGATGTAGAAAGTA
ACTCACTGAAGACATACACCGTTAACCCCAACCAACACTTCTCTCTGTCAACGAAGGAAAGTGCAGATGGAAGTAAATAC
CCGGAATTACTGCTGGAAAAACCTCTAGACAGAGAACGTCAGAGCTCCCATCGCTTAATCCTGACTGCCCTGGACGGAGG
CAACCCGCCTCTAAGCGGCACCACCCAGGTCTGGATCCAAGTCACTGACGCCAACGATAATGCCCCGGTGTTCAGCCAGG
ACGTATACAGGGTTAGCCTCCAAGAAAACGTGCCCCGGGAAACCTCCGTGCTGCGAGTGATGGCCACAGACCAGGACGAG
GGCATTAACGCAGAGCTCACTTATGCCTTTCTCAATTCTCCAAGTACCAGCCTCTTCAATCTCAATCCAAATACTGGCGA
TATCACAACCAATGGTATATTGGACTTTGAAGAGACTAGTAGATATGTGTTGGGTGTGGAAGCCAAGGATGGAGGGGTGC
ACACAGCTCACTGTAATGTTCAGATTGAAATCGTTGATGAGAATGACAATGCCCCAGAGGTGACATTTGTATCCTTTTCT
AACCAGATTTCAGAGGACTCTGACGTTGGAACTGTGATAGCTCTCATAAAAGTGCGAGACCAGGATTCTGGGCAAAATGG
TGTAGTAACCTGCCATATTCAGGAAGACGTTCCCTTCAAGTTAGCATCCACCTCCAAGAATTATTACAAACTAGTGATTG
ACAGGGCCCTAAACCGGGAGCAGACTGCAGACTACAACGTCACCATCACAGCCACAGACCGGGGCAAGCCGCCCCTTTCT
TCAAGGACAAGTGTCACCCTACACATTTCCGACGTCAATGACAACGCTCCTGTTTTCCACCAGGCCTCCTACATGGTCCA
CGTGCCAGAAAACAACCCACCTGGCGCCTCCATTGCGCAGGTCAGCGCCTCGGACCCGGATTTGGGACCCAACGGCCTTG
TCTCCTACTCGATCGTGGCCAGCGACCTGGAGCCGCGGGCGCTGTCGTCCTACGTGTCGGTGAGCGCGCAGAGCGGCGTG
GTGTTCGCGCAGCGCGCCTTCGACCACGAGCAGCTGCGCGCCTTCGAGCTGACGCTGCAGGCCCGCGACCAGGGCTCGCC
CGCGCTGGGCGCCAACGTGAGCCTGCGCGTGCTGGTGGGCGACCGCAACGACAACGCGCCGCGCGTGCTGTACCCCGCGC
TGGGGCCC
ORF - retro_tsyr_692 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.52 % |
| Parental protein coverage: | 99.44 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EQIHYAIPEELAMGALVGNLANDLGFGVRDLPTRNLRVRAEQKFTVSTENGDLLVNDRID-EQICGKKSM |
| .QI.Y.IPEELA.G.LVGNLA.DLG..V..LP.R.LRV.AE..F..S.E.GDLLV..RID.E.ICG.KS. | |
| Retrocopy | QQIQYTIPEELAKGSLVGNLAKDLGLSVQELPARKLRVSAEDYFNISAESGDLLVSGRIDREKICGRKSE |
| Parental | CVLEFEMIAEKPLNFFQVTVLIQDVNDNPPTFSQNITELEISEMALIGATFALESAQDPDVGANSLQQYY |
| C.LEFEM.AE.P.N.F.V.V.IQD.NDN.P.F......LEI.E.AL.G..F.L.SAQD.DV..NSL..Y. | |
| Retrocopy | CALEFEMVAENPMNVFHVIVAIQDINDNAPYFVAKGIDLEICESALPGVKFPLDSAQDADVESNSLKTYT |
| Parental | LSPNPHFSLIQKENPDGRRYPELVLKAPLDREEQPNHHLVLAAVDGGEPSRSCTTQIRVIVADANDNRPI |
| ..PN.HFSL..KE..DG..YPEL.L..PLDRE.Q..H.L.L.A.DGG.P..S.TTQ....V.DANDN.P. | |
| Retrocopy | VNPNQHFSLSTKESADGSKYPELLLEKPLDRERQSSHRLILTALDGGNPPLSGTTQVWIQVTDANDNAPV |
| Parental | FTQDMFRANVQENLPARSSISRVKTTDLDKGVDAEITYAFINIGKAARQLFRLNFNTRELTTSEGLEFEE |
| F.QD..R...QEN.P...S..RV..TD.D.G..AE.TYAF.N.......LF.LN.NT...TT...L.FEE | |
| Retrocopy | FSQDVYRVSLQENVPRETSVLRVMATDQDEGINAELTYAFLN--SPSTSLFNLNPNTGDITTNGILDFEE |
| Parental | RDRYAVGVETKDGEHHTAYCKRQIDVLDENDNAPEITLASESQHLQEDAELETAIALIKTHDLDSGLNGE |
| ..RY..GVE.KDG..HTA.C..QI...DENDNAPE.T..S.S....ED....T.IALIK..D.DSG.NG. | |
| Retrocopy | TSRYVLGVEAKDGGVHTAHCNVQIEIVDENDNAPEVTFVSFSNQISEDSDVGTVIALIKVRDQDSGQNGV |
| Parental | ILC-LKGIFSFKIVRST---HRLVTDGTLDREQIPEYNVTITAT-YSNPPLSSSTSITLHIIDDNDSGPI |
| ..C.......FK..........LV.D..L.REQ...YNVTITAT....PPLSS.TS.TLHI.D.ND..P. | |
| Retrocopy | VTCHIQEDVPFKLASTSKNYYKLVIDRALNREQTADYNVTITATDRGKPPLSSRTSVTLHISDVNDNAPV |
| Parental | SPQASYVIHVPENNQPGASIAQVSASDSDLGPNGQGSYWIAAGDGEPRALSSYVSVSAQSGVVLAQRAF- |
| ..QASY..HVPENN.PGASIAQVSASD.DLGPNG..SY.I.A.D.EPRALSSYVSVSAQSGVV.AQRAF. | |
| Retrocopy | FHQASYMVHVPENNPPGASIAQVSASDPDLGPNGLVSYSIVASDLEPRALSSYVSVSAQSGVVFAQRAFD |
| Parental | HERLRAFELTLQAGDQGSPALSAHVSLRVLVGDRNDNAPRVLYPALGP |
| HE.LRAFELTLQA.DQGSPAL.A.VSLRVLVGDRNDNAPRVLYPALGP | |
| Retrocopy | HEQLRAFELTLQARDQGSPALGANVSLRVLVGDRNDNAPRVLYPALGP |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Tarsius syrichta was not studied using RNA-Seq expression data.
Tarsius syrichta was not studied using ChIP-Seq data.
Tarsius syrichta was not studied using EST data.
Tarsius syrichta was not studied using FANTOM5 data.
retro_tsyr_692 was not experimentally validated.
Retrocopy orthology:
Tarsius syrichta does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mustela putorius furo | ENSMPUG00000008368 | 2 retrocopies | |
| Tarsius syrichta | ENSTSYG00000004901 | 2 retrocopies |
retro_tsyr_692 , retro_tsyr_867,
|
| Xenopus tropicalis | ENSXETG00000032691 | 1 retrocopy |