RetrogeneDB ID: | retro_cfam_800 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 18:24027990..24029541(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000030026 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SCYL2 | ||
| Ensembl ID: | ENSCAFG00000006752 | ||
| Aliases: | None | ||
| Description: | SCY1-like 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:19286] |
Retrocopy-Parental alignment summary:
>retro_cfam_800
CATCCTTTAGAAGAATCCAGAGATTGCTTGGCATTTTGTACCGAACCCATTTTTGCCAGTTTAGCCAATGTTTTAGGTAA
CTGGGAAAATCTACCTTCTTCTGTATCTCTAGACATTAAGGATTATAACCTTTATGATGTCGAAACTAAATATGGTTTGC
TTCAGGTTTCTGAAGGACTGTCATTTTTGCATAGCAGTGTGAAAATGGTCCATGGAAATATTACACCTGAAAATATAATT
TTGAATAAAAGTGAGCCTGGAAATAAGGTGCTTTGATATTTGTGTATCATCAACCAATCCTTGTGAACAAGAGCCTAAGT
TACCTTGTAAAGAATGGGACCCAAATTTACCATCATGTGTCTTCCAAATCGTGAATATTTGGGTCCTGAATACATGCTTC
CGGTGAGCTGTGAAATAGCTAGTGATATGTACTCACTAGGAACTGTCAAGTATGCTGTATTTAATAAAGGAAAACCCATA
TTTGAAGTTAACAAGCACGACATTTACAAGAGTTTTAGTAGACAGTTGGATCAGTTGAGTCGTTTAGGATCTAGCTCACC
TTCAAATATACCCGAGGAAGTCCAAGAACACATAAAACTGCTCTTAAATTAACTCCAACTGTAAGATGAGAAGCAGATCA
AATGACAAAGAATTTCTTCTTCAGTGATGTTGGTGCAATAACACTGCAGTATTCTGAGACCTCATTCCAAAGAGATAATC
TTCAGAAATCACAGTTTCTCAAAGGACTGCCAAAAGTTCTACCAAAACTGCCCAAGCGTGTGCAGGGAATTTGTGCCTTG
TTTGACTTCAGAACTTGTAACCCCTGACATGGTATCTTTTGTTTTGCCCACTGTTCTACTGATTGCCAAAGAAGGCTCCA
AGGAAGCACATGTCAAATTAAGTCTACCTGAACGTGGCTCTGTCTTTAAACAGCAGGAGCCCATCCAGGTTGTTAATTTA
CTTACAAAAAAAAATGGATTTGCTGCTAACCAAAACTCCTCCTGAGGAGATAAAGAGCAATGTCCTACCAATGGTTCACA
CAGCACTAGAGGCTCCTTCCATTCAAATTCAGGAACTCTGTTTAAACATCATTCCAAGCTTTGCAAGTCTTATAGACTAT
GCATTCATGAAAAATTCTTTGATACCAAGAATTAAAAATGCATGTCTGCAAACGTCTTCTCTTGCTGTTCACGTCAATTC
ATTAGCGTGCTTAGGAAAGATTTTGGAATACTTGGATAAGTGGTTTGTACTTGATGACATCCTGCCCTTCTTACCATAAA
TTCCATCCAAGGAACCCACAGTCCTCATGGGAATTTTAGGTACTTACAAATGTACGTTTACTCATAAGAAGTTGGGAATC
ACCAAAGAACAGTGGCTGGAAAAGTATTGGCTCATCTGATTCCCCTGAGTATTGAAAATAATCTTAATCTCAATCAGTTC
AATTCTTTCATTTCTGTCATAAAAGAGACGCTTAACAGATTGGAAACTGAACATAAGACTAAACTGGAGCAACTTCATAT
AATGCAAGAGCAGCAGAAAAGGTTACAAATG
ORF - retro_cfam_800 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.21 % |
| Parental protein coverage: | 57.46 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | HPLEESRDCLAFCTEPVFASLANVLGNWENLPSPVSPDIKEYNLYDVETKYGLLQVSEGLSFLHSSVKMV |
| HPLEESRDCLAFCTEP.FASLANVLGNWENLPS.VS.DIK.YNLYDVETKYGLLQVSEGLSFLHSSVKMV | |
| Retrocopy | HPLEESRDCLAFCTEPIFASLANVLGNWENLPSSVSLDIKDYNLYDVETKYGLLQVSEGLSFLHSSVKMV |
| Parental | HGNITPENIILNKSG-AWK-IMGFDFCVSSTNPSEQEPKFPCKEWDPNLPS-LCLPNPEYLAPEYILSVS |
| HGNITPENIILNKS..AWK.I..FD.CVSSTNP.EQEPK.PCKEWDPNLPS..CLPN.EYL.PEY.L.VS | |
| Retrocopy | HGNITPENIILNKSE<AWK<IRCFDICVSSTNPCEQEPKLPCKEWDPNLPS<MCLPNREYLGPEYMLPVS |
| Parental | CETASDMYSLGTVMYAVFNKGKPIFEVNKQDIYKSFSRQLDQLSRLGSSSLSNIPEEVREHVKLLLN-VT |
| CE.ASDMYSLGTV.YAVFNKGKPIFEVNK.DIYKSFSRQLDQLSRLGSSS.SNIPEEV.EH.KLLLN..T | |
| Retrocopy | CEIASDMYSLGTVKYAVFNKGKPIFEVNKHDIYKSFSRQLDQLSRLGSSSPSNIPEEVQEHIKLLLN<LT |
| Parental | PTVRPDADQMTKIPFFDDVGAVTLQYFDTLFQRDNLQKSQFF-KGLPKVLPKMPKRVIVQRILPCLTSEF |
| PTVR..ADQMTK..FF.DVGA.TLQY..T.FQRDNLQKSQF..K...K.....P.........PCLTSE. | |
| Retrocopy | PTVR*EADQMTKNFFFSDVGAITLQYSETSFQRDNLQKSQFL>KDCQKFYQNCPS--VCREFVPCLTSEL |
| Parental | VNPDMVPFVLPNVLLIAEECTKEEYVKLILPELGPVFKQQEPIQI-LLIFLQKMDLLLTKTPPDEIKNSV |
| V.PDMV.FVLP.VLLIA.E..KE..VKL.LPE.G.VFKQQEPIQ..L.......DLLLTKTPP.EIK..V | |
| Retrocopy | VTPDMVSFVLPTVLLIAKEGSKEAHVKLSLPERGSVFKQQEPIQV>LIYLXXXXDLLLTKTPPEEIKSNV |
| Parental | LPMVYRALEAPSIQIQELCLNIIPTFANLIDYPSMKNALIPRIKNACLQTSSLAVRVNSLVCLGKILEYL |
| LPMV..ALEAPSIQIQELCLNIIP.FA.LIDY..MKN.LIPRIKNACLQTSSLAV.VNSL.CLGKILEYL | |
| Retrocopy | LPMVHTALEAPSIQIQELCLNIIPSFASLIDYAFMKNSLIPRIKNACLQTSSLAVHVNSLACLGKILEYL |
| Parental | DKWFVLDDILPFLQQIPSKEPAVLMGILGIYKCTFTHKKLGITKEQ-LAGKVLPHLIPLSIENNLNLNQF |
| DKWFVLDDILPFL..IPSKEP.VLMGILG.YKCTFTHKKLGITKEQ..AGKVL.HLIPLSIENNLNLNQF | |
| Retrocopy | DKWFVLDDILPFLP*IPSKEPTVLMGILGTYKCTFTHKKLGITKEQ<VAGKVLAHLIPLSIENNLNLNQF |
| Parental | NSFISVIKEMLNRLESEHKTKLEQLHIMQEQQKSLDI |
| NSFISVIKE.LNRLE.EHKTKLEQLHIMQEQQK.L.. | |
| Retrocopy | NSFISVIKETLNRLETEHKTKLEQLHIMQEQQKRLQM |
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 | 52 .58 RPM |
| SRP017611_brain | 0 .00 RPM | 57 .56 RPM |
| SRP017611_kidney | 0 .00 RPM | 52 .17 RPM |
| SRP017611_liver | 0 .00 RPM | 28 .57 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_800 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_800 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_800 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 | ENSCAFG00000006752 | 1 retrocopy |
retro_cfam_800 ,
|
| Sarcophilus harrisii | ENSSHAG00000011140 | 1 retrocopy |