RetrogeneDB ID: | retro_cfam_1709 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 4:64399161..64399863(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RHBDD3 | ||
| Ensembl ID: | ENSCAFG00000012114 | ||
| Aliases: | None | ||
| Description: | rhomboid domain containing 3 [Source:HGNC Symbol;Acc:1308] |
Retrocopy-Parental alignment summary:
>retro_cfam_1709
CTACTGTCCCCAGCGCTACCTCTTGCCTCCTCCATCCTGACGCTGCTGCTGAGCAACCTGTGGCTGGTGGGGGTGGCCCT
CGTCTTACCCTGGCCCCAGAGCTGCTGCTGGACCCTTGGCAGGCTCACTGGCTGCTGGCCCAGGCCCTGGGGTACACGGC
CAGACCTGGCCTGCTCCTGAGCCTGCTGTTCCTGCCCCCACTAGGCTGGTGGCAGCAGTGCTACCTGGGCACACTGAGGC
TCCTGCATGCCCCTGCCCTGCTCCCCCTGGCTGCTGGGCTAATAGGTGTGCTGCTGGCAGGCCTCAAGGTATCCAGTGCA
GCTGGTGGCTATGGCTACATGCCTGTCCACCAGGCCATGCTGGCAGGGCAACGTTACCACCTACACATTCCAAGGGGGTA
CTGCCACTGTGGCTGCTGCCATAGCTGCTGCTTGACTTGACACCACCGCTCAGCTCCAAGCCATCCTTCCTGCAGCTACT
CTGAAGCCTCTTGTTGGCCTGGCCTCTGCAGCCAGGGCCTTCCAGTGGTTGGAGCTCCCTGAGCTGAGGCTGCAAGCACT
GCAGGAGGGCATCTTGTGCAGGGCCCTGGCAGGATGCTGGCCACACAGACTCTGTCCTACCTCTGGTGATCTGGCCCGAG
CTACCTGTCACCCATCCTGTTGGGTGCAGCCTCTTGCCTCTGGACCTCCTTACATGGCCTCT
ORF - retro_cfam_1709 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.75 % |
| Parental protein coverage: | 71.65 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | LPSPALPLASSVLMLLLSSLWLVGA-GPSLALAPELLLDPWQAHRLLTHALGHTALPGLLLSLLLLPTLG |
| L.SPALPLASS.L.LLLS.LWLVG..GP.L.LAPELLLDPWQAH.LL..ALG.TA.PGLLLSLL.LP.LG | |
| Retrocopy | LLSPALPLASSILTLLLSNLWLVGV<GPRLTLAPELLLDPWQAHWLLAQALGYTARPGLLLSLLFLPPLG |
| Parental | WWQECHLGTLRFLHASALLALAAGLMGVLLAGLGVSSAAGGCGYMPVHLAMLAGQGYH-PRQPLGILPPW |
| WWQ.C.LGTLR.LHA.ALL.LAAGL.GVLLAGL.VSSAAGG.GYMPVH.AMLAGQ.YH.P....G.LP.W | |
| Retrocopy | WWQQCYLGTLRLLHAPALLPLAAGLIGVLLAGLKVSSAAGGYGYMPVHQAMLAGQRYH<PTHSKGVLPLW |
| Parental | LLPWLLLALTPLLSSEPPFLQLFCGL-LAGLAYAAGAFQWLELSERRLQALQEGALCRALARCWPFRLLP |
| LLP.LLL.LTP.LSS.P.FLQL...L.L.GLA.AA.AFQWLEL.E.RLQALQEG.LCRALA.CWP.RL.P | |
| Retrocopy | LLP*LLLDLTPPLSSKPSFLQLL*SL<LVGLASAARAFQWLELPELRLQALQEGILCRALAGCWPHRLCP |
| Parental | TPGSLA-ELPVIHPAA-ARPPTPGLPYMAS |
| T.G.LA.ELPV.HP.....P...G.PYMAS | |
| Retrocopy | TSGDLA>ELPVTHPVG<VQPLASGPPYMAS |
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 | 19 .19 RPM |
| SRP017611_brain | 0 .00 RPM | 13 .18 RPM |
| SRP017611_kidney | 0 .00 RPM | 21 .53 RPM |
| SRP017611_liver | 0 .00 RPM | 6 .31 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1709 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1709 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1709 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 | ENSCAFG00000012114 | 1 retrocopy |
retro_cfam_1709 ,
|
| Gorilla gorilla | ENSGGOG00000012202 | 1 retrocopy |