RetrogeneDB ID: | retro_cfam_1008 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 21:16651678..16653324(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NOC3L | ||
| Ensembl ID: | ENSCAFG00000008033 | ||
| Aliases: | None | ||
| Description: | nucleolar complex associated 3 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24034] |
Retrocopy-Parental alignment summary:
>retro_cfam_1008
AGAAGAAATAAAAAACAGATCCTAAGCTTTTGGAAGTTTCTAAAGACTAGTAAAGTCAGACTTGAAAACAAGTTGAAAAA
TAAGCAATTTAAACCACAAAGCACTGTCTAGAAGTACTGAAAAGAACAGAGGAAACTAAGGCAGCTGTAAAGGATGTTGT
GTCTAAGAAACCGATCCCACTGGAGGACCTGAAGGAGAAAAGACCAGGTAAAAGAATTGAGAGGGAAGAGGAGGAAGAAG
AGGAAGCACTTCCTTTGGATATGATGAATGAAGATGACTTGCAGTTAATGATAGAGTTAGGACAAAGAGCCTCTTTTCTA
ACGAGAGATCTTTCTTCTAGCGAACCTGTTCACTCCAAGAAACGAAAGCATGAGCATGTTATAGATAAATATGAAAAAAT
ACCAAGAACTCTGCAAACTGCACCAGAGAAGGAACTGATTCACTTGCTTCCCATCAAGGATAAAAGTGGTATAATCCCAC
AGACCAGGGAGAAGCAAGTTACTGACAATAACCAAGATGAAGAGGATCAAGAAGAGGTGGAACTTGAGGAAGAGATTGTT
GAAGATCCCATTCGAGAACTGACATTAGAAGAACATGTAATTGAAAGAAGGAAGAAGCTATAGGATAAGAAAATGCATAT
TGCAGCTTTGGCATCTGCCATATTATCAGATCCAGAAACTAATATTAAAAAATTGAAAGAACTACGTTCTATGCTGATGG
AACAGGATCCTGATGTGGCTGTTACTGTTCAAAAGCTGGTGATAGTTTCCCTGATGGAGTTATTTAAAGACATTACTCCT
TCATATAAAATACAACCCCTCAGAAGAAGAAAAATCCACCAAGATCCTCAAAGAAACCCCCAAATTAAGAGAATTTGAAG
AAGGCCTGGTTAGCCAATGTAAATTTTATTTGGAAAATATGGAGCAAATGATTAAAGACTAGAAGCAAAGGAAACTGAAG
AAAAGTAATGTATTTTCCTTAAAGGCCTACAAAGGACTGGCGGAAGTGGCTGTGAAGAGCCTGTGTGAGCTGTTGGTGTC
ACTACCTCATTTCAACTTTCACAACAACATCATTGTATTGATTGTCCCTCTCATGAATGATGTATCAAAGTCGATCTCTG
GAATGTGTTGTGAGGCAGTAAAGAAATGGTTTAAGCAAGATAAATTAGGCCAAGCTTCCCATGGTGTGATTAAAGTGATT
TCTGGTTTTGTGAAGGGCAGAAATTATGAAGTTAGGTCAGAGATGTTAAAGACATTATTGTGCTTAAGAAATCAGGAAGT
AGAAGTGAAAAAAGATACAGAGGACATTAATAAACCAAAAAAGTTCATGACTTTCAAGGAAAAGAGAAAAACTATCAAGA
ATGCAGAAAAAGTGGAATAAAGCAGAAGAGAAACTAGAGCGAGAGCTTCTGGAGGCAGAAGCTTCAGAGAACACAGAGAG
AAAACTTAAACTGCACATGGAGACTCTGAATATTGTGTTTGTAACCTACTTCAGAATATTGAAGAAGGCCCAGAGTGTAA
CCTCTCCTGCCAGCAGTTCTAGAAGGCCTTGCCAAGTTGGCTTATCTTATAAAAGTGGAGTTTTTTGATGATTTATTAGT
AGTACTTCATACTCTCATTGAGTCTGGTGATCTAAGCTATGGAGAA
ORF - retro_cfam_1008 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.29 % |
| Parental protein coverage: | 68.84 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | RRNKKQIPSFRKLLKTSKVKLENKLKNKQFKQQSTLKKYRKEQRKLRQ-AVKDAVSKKPIPLEDPKEKRP |
| RRNKKQI.SF.K.LKTSKV.LENKLKNKQFK.QST..KY.KEQRKLRQ.AVKD.VSKKPIPLED.KEKRP | |
| Retrocopy | RRNKKQILSFWKFLKTSKVRLENKLKNKQFKPQSTV*KY*KEQRKLRQ<AVKDVVSKKPIPLEDLKEKRP |
| Parental | GKRIEREEEEEEEALPLDMMDEDDLQLMRELGQRASFLTRDLSSSEPVHAKKRKYERVIDKYEKIPRTLQ |
| GKRIEREEEEEEEALPLDMM.EDDLQLM.ELGQRASFLTRDLSSSEPVH.KKRK.E.VIDKYEKIPRTLQ | |
| Retrocopy | GKRIEREEEEEEEALPLDMMNEDDLQLMIELGQRASFLTRDLSSSEPVHSKKRKHEHVIDKYEKIPRTLQ |
| Parental | TAPEKEMIHLLPIKDKSGIIPQTREKPVIDNNQDEEDQEEVELEEEIVEDPIRELTLEEHLIERRKKLQE |
| TAPEKE.IHLLPIKDKSGIIPQTREK.V.DNNQDEEDQEEVELEEEIVEDPIRELTLEEH.IERRKKL.. | |
| Retrocopy | TAPEKELIHLLPIKDKSGIIPQTREKQVTDNNQDEEDQEEVELEEEIVEDPIRELTLEEHVIERRKKL*D |
| Parental | KKMHIATLASAILSDPETNIKKLKELRSMLMEQDPDVAVTVRKLVIVSLMELFKDITPSY-KIRPLTEAE |
| KKMHIA.LASAILSDPETNIKKLKELRSMLMEQDPDVAVTV.KLVIVSLMELFKDITPSY.K..P..E.E | |
| Retrocopy | KKMHIAALASAILSDPETNIKKLKELRSMLMEQDPDVAVTVQKLVIVSLMELFKDITPSY>KYNP-SEEE |
| Parental | KSTKIRKETQKLREFEEGLVSQYKFYLENLEQMVKDWKQRKLKKSNVVSLKAYKGLAEVAVKSLCELLVS |
| KSTKI.KET.KLREFEEGLVSQ.KFYLEN.EQM.KD.KQRKLKKSNV.SLKAYKGLAEVAVKSLCELLVS | |
| Retrocopy | KSTKILKETPKLREFEEGLVSQCKFYLENMEQMIKD*KQRKLKKSNVFSLKAYKGLAEVAVKSLCELLVS |
| Parental | LPHFNFHNNIIVLIVPLMNDVSKSISEMCCEAVKKLFKQDKLGQASLGVIKVISGFVKGRNYEVRPEMLK |
| LPHFNFHNNIIVLIVPLMNDVSKSIS.MCCEAVKK.FKQDKLGQAS.GVIKVISGFVKGRNYEVR.EMLK | |
| Retrocopy | LPHFNFHNNIIVLIVPLMNDVSKSISGMCCEAVKKWFKQDKLGQASHGVIKVISGFVKGRNYEVRSEMLK |
| Parental | TFLCLRIKELEVKKDTEDINKP-KKFMTFK-EKRKTLSRMQRKWKKAEEKLERELLEAEASESTERKLKL |
| T.LCLR..E.EVKKDTEDINKP.KK...F...KR..LSRMQ.KW.KAEEKLERELLEAEASE.TERKLKL | |
| Retrocopy | TLLCLRNQEVEVKKDTEDINKP<KKVHDFQ<RKREKLSRMQKKWNKAEEKLERELLEAEASENTERKLKL |
| Parental | HTETLNIVFVTYFRILKKAQRS-PLLPAVLEGLAKFAHLINVEFFDDLLVVLHTLIESGDLSYRE |
| H.ETLNIVFVTYFRILKKAQ...PLLPAVLEGLAK.A.LI.VEFFDDLLVVLHTLIESGDLSY.E | |
| Retrocopy | HMETLNIVFVTYFRILKKAQSV>PLLPAVLEGLAKLAYLIKVEFFDDLLVVLHTLIESGDLSYGE |
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 | 12 .56 RPM |
| SRP017611_brain | 0 .00 RPM | 9 .37 RPM |
| SRP017611_kidney | 0 .00 RPM | 11 .23 RPM |
| SRP017611_liver | 0 .00 RPM | 7 .83 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1008 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1008 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1008 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 | ENSCAFG00000008033 | 1 retrocopy |
retro_cfam_1008 ,
|
| Rattus norvegicus | ENSRNOG00000013965 | 1 retrocopy |