RetrogeneDB ID: | retro_acar_108 | ||
Retrocopy location | Organism: | Anole lizard (Anolis carolinensis) | |
| Coordinates: | 3:94514073..94515178(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | USP14 | ||
| Ensembl ID: | ENSACAG00000008213 | ||
| Aliases: | None | ||
| Description: | Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:G1KHK9] |
Retrocopy-Parental alignment summary:
>retro_acar_108
TTACACTCTGTGCCAGAACTGAAAGAAGCTCTTAAGAGGTATGCTGGTGCATTAAGAGCTTCAGGGGAAATGGCCTCTGA
TCAGTATATTACTCCAGCTCTTAAGAGATTTATTTTATTCCATTGATAAAACCTCCTCTAGTATCATCATTCTCCTCCAG
TTTTAACACATGGCCTTTCCTCAGTTCACTGAGAAAGACGATCAAGGCCAGTATCTTCAACAGGGTGGTGACGAATGTTG
GGTACAGATGATGTGAGAACTGCAGCAGAAGATAGAAGGGATAGAAGGCGATTCAGTTGTGGAAACTGACCCTGGAGCTT
CATGAGCAGCTGGCTGCACCTCCTCAGAAAATGAGCTTAATTGATCAGTTGTTCAGTATTGAATTTGAAACTACCATGAA
ATGTATAGAAGCAGAAGAGGAGGATATCACAAAAGGAAGAGATAATCAATTCCAACTTAGTTACTTAATCATTCAAGAAG
TTAAATATCTTTTCACTGGTCTTAAACTGCGCCTTCAAGAAGAAATCATCAAACTGTCTCCAACCTTGCAAAAAAAATGC
ATTTCACATTTTTTTTCCAAAATAAGTCACCTGCCTGCTTACCTGACTATTCAGATGGCTTTTACAAAGAGAGAGAATCT
GTAAATGCAAAAGTTCCCAAGGATGTTAAGTTTTTTCTTATGTTGGATGTATATGATTTATGTAGATCAGAACTTCAAGA
GAACATGGATGCCTACCAATCAAAATTCAAGGACTTGAAAGACAAGAAAGTGAAACAAACAAAGCATTCTCGTAAAGGTG
ATGTTGCACAGAAAAAAGTTAAACATGAAGCATTTTCCTTTCCTGATGATATTGCCTCCAATATCTGTGGTTATTATGAA
CTGCAGGCTGTGTTAACACATCAAGGAAAATTTAGTTCTTCTGGACACTATGTATCTTTGGTTAAAAGAAAAGAAGATGA
ATTGATCAAATTTCATGATGACAAAGTCAGCACTGTTACACCAGAAGAAAACTTGAGGTTATGTGGGGGTGGAGACTGGC
ATATAGCTTACATCCTATTTTATGGGCCACACAGAATTAAAGTAATAAAAGATGAAGATGAACAA
ORF - retro_acar_108 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.39 % |
| Parental protein coverage: | 75.35 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | IRSVPELKEALKRYAGALRASGEMASAQYITAAL-RDLFDSMDKTSSSIPPIILLQFLHMAFPQFAEKGD |
| ..SVPELKEALKRYAGALRASGEMAS.QYIT.AL.RDLF.S.DKTSSSI..IILLQF.HMAFPQF.EK.D | |
| Retrocopy | LHSVPELKEALKRYAGALRASGEMASDQYITPAL>RDLFYSIDKTSSSI--IILLQF*HMAFPQFTEKDD |
| Parental | QGQYLQQDANECWVQMMRVLQQKLEGIEGDTVMETDPGASGAA-AAPPKKKSLIDQFFSIEFETTMKCTE |
| QGQYLQQ...ECWVQMM..LQQK.EGIEGD.V.ETDPGAS.AA.AAPP.K.SLIDQ.FSIEFETTMKC.E | |
| Retrocopy | QGQYLQQGGDECWVQMM*ELQQKIEGIEGDSVVETDPGAS*AA>AAPPQKMSLIDQLFSIEFETTMKCIE |
| Parental | AEEEEVTKGRENQLQLSCFINQEVKYLFTGLKLRLQEEITKLSPTLQRNALYIKSSKISRLPAYLTIQMV |
| AEEE..TKGR.NQ.QLS..I.QEVKYLFTGLKLRLQEEI.KLSPTLQ........SKIS.LPAYLTIQM. | |
| Retrocopy | AEEEDITKGRDNQFQLSYLIIQEVKYLFTGLKLRLQEEIIKLSPTLQKKCISHFFSKISHLPAYLTIQMA |
| Parental | RFFYKEK-ESVNAKVLKDVKFPLMLDVYELCTPELQESMVPYRSKFKDLEDKKVNQQTKNSSKGDGAQKE |
| ..F.K...ESVNAKV.KDVKF.LMLDVY.LC..ELQE.M..Y.SKFKDL.DKKV..QTK.S.KGD.AQK. | |
| Retrocopy | --FTKRE<ESVNAKVPKDVKFFLMLDVYDLCRSELQENMDAYQSKFKDLKDKKV-KQTKHSRKGDVAQKK |
| Parental | VKYEAFSFPDDIGSNNCGYYELQAVLTHQGRSSSSGHYVSWVKRKEDEWIKFDDDKVSTVTPEDILRLSG |
| VK.EAFSFPDDI.SN.CGYYELQAVLTHQG..SSSGHYVS.VKRKEDE.IKF.DDKVSTVTPE..LRL.G | |
| Retrocopy | VKHEAFSFPDDIASNICGYYELQAVLTHQGKFSSSGHYVSLVKRKEDELIKFHDDKVSTVTPEENLRLCG |
| Parental | GGDWHIAYVLLYGPRRIEVMEEEAEQ |
| GGDWHIAY.L.YGP.RI.V...E.EQ | |
| Retrocopy | GGDWHIAYILFYGPHRIKVIKDEDEQ |
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 |
|---|---|---|
| SRP009831_adrenal | 0 .00 RPM | 49 .27 RPM |
| SRP009831_brain | 0 .00 RPM | 44 .88 RPM |
| SRP009831_dewlap | 0 .00 RPM | 134 .79 RPM |
| SRP009831_embryo | 0 .00 RPM | 145 .35 RPM |
| SRP009831_heart | 0 .00 RPM | 50 .33 RPM |
| SRP009831_liver | 0 .00 RPM | 31 .29 RPM |
| SRP009831_lung | 0 .00 RPM | 33 .90 RPM |
| SRP009831_ovary | 0 .00 RPM | 143 .43 RPM |
| SRP009831_skeletal_muscle | 0 .00 RPM | 69 .20 RPM |
Anolis carolinensis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_acar_108 retrocopy.
Anolis carolinensis was not studied using FANTOM5 data.
retro_acar_108 was not experimentally validated.
Retrocopy orthology:
Anolis carolinensis 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 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Anolis carolinensis | ENSACAG00000008213 | 1 retrocopy |
retro_acar_108 ,
|
| Choloepus hoffmanni | ENSCHOG00000010588 | 4 retrocopies | |
| Echinops telfairi | ENSETEG00000004949 | 1 retrocopy |