RetrogeneDB ID: | retro_cfam_370 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 10:29792..31550(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000000049 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAP1GDS1 | ||
| Ensembl ID: | ENSCAFG00000010267 | ||
| Aliases: | None | ||
| Description: | RAP1, GTP-GDP dissociation stimulator 1 [Source:HGNC Symbol;Acc:9859] |
Retrocopy-Parental alignment summary:
>retro_cfam_370
GCAGATACTCTCAGTGATACCTTGAAGAAGTTGAAGATAACAGCTGTTGACAGAACCGAAGATAGTTTAGAAGGATGCTT
GGATTGTCTGCTTCAAGCCCTGGCTCAAAATAATATGGAAACGAGTGAAAAAAATCCAAGGAAGTGGAATACTTCAGCTG
TTTGTAAGTCTGTTGATTCCACAGTCTTCCTGCACAGCCAAAGTAGCTAATGTCATAGCAGAAGTAGCCAAAAATGAATG
TATGCGTATTCCATGTATGGATACTGGATTGACTTCACCATTGGTGCAGCTGCTAAATAGCAAAGACCAGGAAGTGCTAC
TTCAAATGGGCAGGGCTCTGGGAAGCATATGTTACGATAGCCATGAGGGCAGAAGTGCAGTTGATCAAGCAGGTGGTGCA
CAGATTGTAATTGACCATTTAAGGTCACTATGCAGTATAACAGATCCCACCAATGAAAAGCTCTTGACTGTCTTTTGTGG
TATGCTGATGAACTACAGCAATGAGAAAGATTCCCTTCAAGCTCAGCTTATCAATATGGGTGTTATACCTACCGCAGTGA
AATTACTGGGCATCCATTGCCAAAATGCAGCTCATACAGAAATGTGTCTTGTTGCATTTGGTAACTTAGCAGAACTTGAG
TCAAGTAAAGAACAGTTTGCCAGTACGAACGTTGCTGAAGAGCTAGTAAAACTCTTTAAGAAACAAATAGAACATGATAA
AAAGGAAATTATTTTGGAAGTTCTTTCTCTACTGGCAGAAAATGATGCTATTAAACTACATCTGGTTGAAGCAGGCCTGG
TAGAGTGTCTACTACAGATTGTTCAGCAGAAAGTGGATAGTGACAAAGGGCATGATATTGCTGAGCTCAAAACCGCTTCA
GATCTAATGGTTTTTCTACTTCTTGGATTTGAATCCATGCAGAAATTATTTGAAGAAGGAAAAGGTAATGTGTTTCAAAG
GGTGCTGTCCTGGATTCCATTAAATAACCACCAGCTACAGCTTGCTGGAGCATTGGCAATTGCAAATTTTGCCAGAAACG
GTGGAAACTGTATCCACATGGTAGACAATGGAATTGTAGAAAAACTTATGGATTTACTGGACAGACATGTAGAAGATGGG
AATGTAACTGTACAGCATGCAGCATTAATGACCTCAGAAATCTCGCCATTCCAGTTGTAAAAAAAGCAAAGATGTTATCA
GCTGGAGTCACAGAGGCAGTTTTGAAATTCCTTAAGTCTGAAATGCCTCCAATTCAGTTCAAACTTTTGGGAACCTTAAG
AATGTTAATAGATGCACAAGCAGAAGCTGCTGAACAACTGGGAAAGAATGTTAAATTAGTGGAGCGTTTGGTAGAATGGT
GCAAAGCCAAAGATCATGCTGGTGTGATGGGGGAGTCCAACAGACTGCTGTCTGCCCTCATTCATCACAATAAATCAAAA
GATGTAATTAAAACCATTGTACAGAGTGGTGGCACCAAGCATCCTGTTACCATGGCAACTAGTGAACATGTAGTAATGCA
GAATGAAGCCCTTGTTGCTTTGGCACTAATAGCAGCTTTAGAGTTGAGCACTGCTGAGAAAGATCTAGAAAGTGCTAAAC
TTGTACAGAATTCACACAGACTGCTGGAAGATGAAAGAAGTGCTCCGGAAATCAAATATAATTCCACGGTCCTTATTTGT
GCTCTCATGGGATCTGAATCTCTACAAAAGGAAGTACAGGATTTGGCCTTTCTAGAGGTTGTATCTAAACATCGCAGT
ORF - retro_cfam_370 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.82 % |
| Parental protein coverage: | 96.54 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | ADNLSDTLKKLKITAVDRTEDSLEGCLDCLLQ-PWLKIDMETSEKIQGSGILQLFASLLIPQSSCTAKVA |
| AD.LSDTLKKLKITAVDRTEDSLEGCLDCLLQ.PWLKI......KIQGSGILQLF.SLLIPQSSCTAKVA | |
| Retrocopy | ADTLSDTLKKLKITAVDRTEDSLEGCLDCLLQ>PWLKIIWKRVKKIQGSGILQLFVSLLIPQSSCTAKVA |
| Parental | NIIAEVAKNEFMRIPCVDAGLISPLVQLLNSKDQEVLLQTGRALGNICYDSHEGRSAVDQAGGAQIVVDH |
| N.IAEVAKNE.MRIPC.D.GL.SPLVQLLNSKDQEVLLQ.GRALG.ICYDSHEGRSAVDQAGGAQIV.DH | |
| Retrocopy | NVIAEVAKNECMRIPCMDTGLTSPLVQLLNSKDQEVLLQMGRALGSICYDSHEGRSAVDQAGGAQIVIDH |
| Parental | LRSLCSITDPANEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTLVKLLGIHCQNAALTEMCLVAFGNL |
| LRSLCSITDP.NEKLLTVFCGMLMNYSNE.DSLQAQLINMGVIPT.VKLLGIHCQNAA.TEMCLVAFGNL | |
| Retrocopy | LRSLCSITDPTNEKLLTVFCGMLMNYSNEKDSLQAQLINMGVIPTAVKLLGIHCQNAAHTEMCLVAFGNL |
| Parental | AELESSKEQFASTNIAEELVKLFKKQIEHDKREMIFEVLAPLAENDAIKLQLVEAGLVECLLEIVQQKVD |
| AELESSKEQFASTN.AEELVKLFKKQIEHDK.E.I.EVL..LAENDAIKL.LVEAGLVECLL.IVQQKVD | |
| Retrocopy | AELESSKEQFASTNVAEELVKLFKKQIEHDKKEIILEVLSLLAENDAIKLHLVEAGLVECLLQIVQQKVD |
| Parental | SDKEDDIAELKTASDLMVLLLLGDESMQKLFEGGKGNVFQRVLSWIPSNNHQLQLAGALAIANFARNDGN |
| SDK..DIAELKTASDLMV.LLLG.ESMQKLFE.GKGNVFQRVLSWIP.NNHQLQLAGALAIANFARN.GN | |
| Retrocopy | SDKGHDIAELKTASDLMVFLLLGFESMQKLFEEGKGNVFQRVLSWIPLNNHQLQLAGALAIANFARNGGN |
| Parental | CIHMVDNGIVEKLMDLLDRHVEDGNVTVQHAAL-SALRNLAIPVVNKAKMLSAGVTEAVLKFLKSEMPPV |
| CIHMVDNGIVEKLMDLLDRHVEDGNVTVQHAAL...LRNLAIPVV.KAKMLSAGVTEAVLKFLKSEMPP. | |
| Retrocopy | CIHMVDNGIVEKLMDLLDRHVEDGNVTVQHAAL<NDLRNLAIPVVKKAKMLSAGVTEAVLKFLKSEMPPI |
| Parental | QFKLLGTLRMLIDAQAEAAEQLGKNVKLVERLVEWCEAKDHAGVMGESNRLLSALIRHSKSKDVIKTIVQ |
| QFKLLGTLRMLIDAQAEAAEQLGKNVKLVERLVEWC.AKDHAGVMGESNRLLSALI.H.KSKDVIKTIVQ | |
| Retrocopy | QFKLLGTLRMLIDAQAEAAEQLGKNVKLVERLVEWCKAKDHAGVMGESNRLLSALIHHNKSKDVIKTIVQ |
| Parental | SGGIKHLVTMATSEHVIMQNEALVALALIAALELGTAEKDLESAKLVQILHRLLEDERSAPEIKYNSMVL |
| SGG.KH.VTMATSEHV.MQNEALVALALIAALEL.TAEKDLESAKLVQ..HRLLEDERSAPEIKYNS.VL | |
| Retrocopy | SGGTKHPVTMATSEHVVMQNEALVALALIAALELSTAEKDLESAKLVQNSHRLLEDERSAPEIKYNSTVL |
| Parental | ICALMGSESLHKEVQDLAFLDVVSKLRS |
| ICALMGSESL.KEVQDLAFL.VVSK.RS | |
| Retrocopy | ICALMGSESLQKEVQDLAFLEVVSKHRS |
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 .04 RPM | 56 .36 RPM |
| SRP017611_brain | 0 .24 RPM | 106 .78 RPM |
| SRP017611_kidney | 0 .07 RPM | 12 .08 RPM |
| SRP017611_liver | 0 .00 RPM | 8 .92 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_370 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_370 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_370 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000010267 | 2 retrocopies |
retro_cfam_1428, retro_cfam_370 ,
|