RetrogeneDB ID: | retro_cfam_1704 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 4:57977189..57977867(-) | ||
| Located in intron of: | ENSCAFG00000017902 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RABEPK | ||
| Ensembl ID: | ENSCAFG00000020201 | ||
| Aliases: | None | ||
| Description: | Rab9 effector protein with kelch motifs [Source:HGNC Symbol;Acc:16896] |
Retrocopy-Parental alignment summary:
>retro_cfam_1704
GATTTAGCCACCTTGGAGGGCCTCTTGCCCCATTCCAAGCATGCCGGCTTTGTTCTTTCTTATGCACCTCACAGCGTGTG
GGTGTTTGGAGGTGATGACTAGTCAGGAAATTGAAATTGCCTACAAGTTCTGAATCCTGAAACTAGGACTTTGGGACCAT
GCCAGAGGTGAGCAATCCCCCACTGTTCCCAAGACCATTCACACATCATCTGAAGCCACTGGAAACCAGTTGTATATCTT
TGTGGGTGGAAAGAGAGGCACCCAGCCCATGCAGGATGTGAAGCTGCATGTGTTTGATGCAAACACTCTGACCTGGTCAC
AGACAGACACACGTGGAAAACTTCCAATCTCCCGGGCATGGTCATGTGGTGGTGGCAGCAGGGACAAAGCTCTTCATCCC
TGGAGGCTTGGCAGGGGACAGATTCTATGATGATGTGATTGCACTGACACAAGTGACCAGAAGTAGCAGAAACTAAGTCC
CACTGGGGCACCTCCCACAGGCTGCGCTGTCCACTCAGCTGTGGCTTTGGGGAAACACCTGTATCATCTTTGGAGGGGTG
ACTCCCACAGGAGCACTGGATACAATGTACCAATCTCACATAGAAAAGCAGCATCTGGGGGACCTTGCATAAATTTGAAA
CTTTTCTACCACCTGGACCATTGGATCATTCTATGTGT
ORF - retro_cfam_1704 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.71 % |
| Parental protein coverage: | 60.22 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | DLATSEGLLPRYEHASFVPSCAPHTIWVFGGADQSGNRNCLQILNPATRT-W-TMPEVTS-CPPSPRTLH |
| DLAT.EGLLP...HA.FV.S.APH..WVFGG.D.SGN.NCLQ.LNP.TRT.W.TMPEV....P..P.T.H | |
| Retrocopy | DLATLEGLLPHSKHAGFVLSYAPHSVWVFGGDD*SGN*NCLQVLNPETRT>W>TMPEVSN<SPTVPKTIH |
| Parental | TSSAAIGNQLYVFGGGERGAQPVQDVKLHVFDANSLTWSQPETLGKPP-SPRHGHVMVAAGTKLFIHGGL |
| TSS.A.GNQLY.F.GG.RG.QP.QDVKLHVFDAN.LTWSQ..T.GK.P.SP.HGHV.VAAGTKLFI.GGL | |
| Retrocopy | TSSEATGNQLYIFVGGKRGTQPMQDVKLHVFDANTLTWSQTDTRGKLP>SPGHGHVVVAAGTKLFIPGGL |
| Parental | AGDKFYDDL-HCIDIRDMKWQELSPTGAPPTGCAAHSAVAVGKHLY-IFGGMTPTGALDTMYQYHIEKQH |
| AGD.FYDD...C.D..D.K.Q.LSPTGAPPTGCA.HSAVA.GKHLY.IFGG.TPTGALDTMYQ.HIEKQH | |
| Retrocopy | AGDRFYDDV<DCTDTSDQK*QKLSPTGAPPTGCAVHSAVALGKHLY>IFGGVTPTGALDTMYQSHIEKQH |
| Parental | -W-TLLKFDNFLPPGRLDHSMC |
| .W.TL.KF..FLPPG.LDHSMC | |
| Retrocopy | >WGTLHKFETFLPPGPLDHSMC |
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 |
|---|---|---|
| SRP012049_cerebellum | 0 .00 RPM | 44 .90 RPM |
| SRP017611_brain | 0 .00 RPM | 26 .36 RPM |
| SRP017611_kidney | 0 .00 RPM | 42 .59 RPM |
| SRP017611_liver | 0 .00 RPM | 18 .78 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1704 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1704 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1704 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 | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000020201 | 1 retrocopy |
retro_cfam_1704 ,
|
| Callithrix jacchus | ENSCJAG00000006849 | 1 retrocopy |