RetrogeneDB ID: | retro_cfam_1713 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 4:78878973..78879765(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | EHD1 | ||
| Ensembl ID: | ENSCAFG00000014128 | ||
| Aliases: | None | ||
| Description: | EH-domain containing 1 [Source:HGNC Symbol;Acc:3242] |
Retrocopy-Parental alignment summary:
>retro_cfam_1713
CCCATGCTACTTCTCGTGGGCTAGTGCAGCACTGGCAAGACCACCTTCATCTGGCCCCTGATCCAACAGGCCTTCCCAGG
AGTTGGCATCTGGCCTTGCACACCACTGATGCCTTCATTTCCCAGGGGCACAGCCTCACCAAGGGCCTGGTGCCTGGCCA
CATGCTTGGGTGGATGCATGGAGCCCCATCTGCCAGCTCAACGAAGTTGGGCAACAGGTTCCTCAGCAGGTTCACAGGTG
CCTCCCACCCATCCCAGTGTAGGACAGCATATGCATCACAGACACTCCCGGGATGCTGTCTTGAGAGAAGTAGGGCATCA
GCAGAGGTTATGGCTGGGGGTGGTCCTGGAGTAGTTGGCTGAATGTATCTACCGCATTGTACCATTTTTTGAGACCATTT
GGTGGACACCTTTGAAGAGTTCTCCTAAGTCATCATGGCCCTGAAAAACCAGAAGGACAAGATATGGGGGATGGTGAACA
AGAGCTACCCAACAGAGACCCATCAGCCCGTCTTGGGGGTGGGGTTGTAGTCTCTGGGAAAGATCAACCCCCCTGAGGTG
GTCAGCTGCTTCTGCTTCCACCTGCTTCTAATCTCTGACATCCATGGGCTCTCCTAGGCTGAGGAGCAGGGCCTGCTAAA
AGACATCCAGTCTCTGCCCCCAAATACTGTCCTCAAAAAACTCAGTGAATTAAACAAGTGGGTATGGCTGGCCAACATCC
ATGCCTACCTACATCATTAGCTCCCTTAAGGAGGAAGTGTTCAATGTCTTCAGTAAACAGAGCAAAAAGAAA
ORF - retro_cfam_1713 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.26 % |
| Parental protein coverage: | 57.54 % |
| Number of stop codons detected: | 8 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | PMVLLVGQYSTGKTTFIRHLIEQDFPGMRIGPEP-TTDSFIAVMHGPTEGVVPGNALVVDPRRPFRKLNA |
| PM.LLVG..STGKTTFI..LI.Q.FPG..I.P...TTD.FI...H..T.G.VPG..L......P...... | |
| Retrocopy | PMLLLVG*CSTGKTTFIWPLIQQAFPGVGIWPCT<TTDAFISQGHSLTKGLVPGHMLGWMHGAPSASSTK |
| Parental | FGNAFLNRFMCAQLPN-PVLDSISIIDTPGILSGEKQRISRGYDFA-AVLEWFAERVDRIILLFDA-HKL |
| .GN.FL.RF..A..P..PV.DSI.I.DTPG.LS.EK..ISRGY.....VLE..AE...RI...F...H.. | |
| Retrocopy | LGNRFLSRFTGASHPS<PV*DSICITDTPGMLS*EK*GISRGYGWG<VVLE*LAECIYRIVPFFET<HLV |
| Parental | DISDEFSEVIKALKNHEDKIRVVLNKADQIETQQLMRVYGALMWSLGKIINTPEVVRVYIGSFWSHPLLI |
| D...EFS.VI.ALKN..DKI....NK....ET.Q...V.G....SLGKI.N.PEV.......F..H.LLI | |
| Retrocopy | DTFEEFS*VIMALKNQKDKIWGMVNKSYPTETHQ--PVLGVGL*SLGKI-NPPEV----VSCFCFHLLLI |
| Parental | PDNRKLFEAEEQDLFKDIQSLPRNAALRKLNDLIKRARLAKVHAYI-ISSLKKE-MPNVFGKESKKK |
| .D...L..AEEQ.L.KDIQSLP.N..L.KL..L.K...LA..HAY..I.S..KE...NVF.K.SKKK | |
| Retrocopy | SDIHGLS*AEEQGLLKDIQSLPPNTVLKKLSELNKWVWLANIHAYL>IISSLKEEVFNVFSKQSKKK |
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 | 68 .50 RPM |
| SRP017611_brain | 0 .00 RPM | 35 .25 RPM |
| SRP017611_kidney | 0 .00 RPM | 64 .91 RPM |
| SRP017611_liver | 0 .00 RPM | 29 .37 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1713 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1713 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1713 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000014128 | 1 retrocopy |
retro_cfam_1713 ,
|
| Callithrix jacchus | ENSCJAG00000002660 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000005706 | 1 retrocopy |