RetrogeneDB ID: | retro_cjac_1829 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:100851953..100853144(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RUFY3 | ||
| Ensembl ID: | ENSCJAG00000014529 | ||
| Aliases: | None | ||
| Description: | RUN and FYVE domain containing 3 [Source:HGNC Symbol;Acc:30285] |
Retrocopy-Parental alignment summary:
>retro_cjac_1829
GGTCTGAATCACACTGATGCCAATTTCTGTATGAAAGGAGAAGACTTGGAATCTCAGGTAGGAGTTATAGATTTTTCAGT
GTATCTCAAGGACAGAACAGCAGTAAAGGTAGTGAAGGAGACAGTCAGATTACTGCAATCCGGACCAGAAGAACTACCTA
GAAGAACTGAACAGATATTTGAATGCTACTGTAAACAACCTTCAGGCAAAAGTAGATGCATTAGAAAAATCGAACACTAA
ACTGACAGGAGCTTGAAGTTGCAAACAACAGGATTATTGCCTTATAAGAAGAAATGGAACAAGTTAAAGAGGAAAGTTCC
TACATACTGGAATCCAATCAGAAGGGTCCCAAGCAAGACAGAACTTCAGAAGGGCAAGCACTAAGTGAAGCAAGAAAGCA
TTTAAAAAAAAGAGACACAATTACAATTGGATGTTGAAAAAGAACTGGAGACGCAGATCAGCATGAAGCAGGAGATGGAA
TTGGCTAAGAAGATGCTGGAGAAGGATGTCTGTGAGAAGCAGGATGCTCTGGTATCTCTTCGGCAGCAGCTGCATGATCT
CAGGGATCTCAACCACGAACTTGCTTTTAAGCTGCAGAGTTCAGACTAAGGAGTAAAACAGAAAAGTGAACTAAACAGTC
TCTTGGAAAATTAATTGATGGCTGCTACCATTAAACAACTAGAACAAAGATTGCACCAGGCTGAGCGAAGCTGCAAGTCT
GCTGAGTTGGACAAGCAGCTCTTCAAACAGGACTTTGAAGACAAGATCAACAGTCTGCAGCTGAAAGTAGAGGATCTCAC
CAGGCAGTGGAACCAGCTTGAATTAGAACTAAAACAGGAAAAAGAAAGATAACAAAATGACAGAAGCATCCCAGGAAAGG
GTTACCAGAAGCCAGAATCTAAGACGGATGGGTAGCACAAAATGCTAGAGGGAAATTTTAAACTAAAAAAGCCCCTGGAA
GAAAGACACAGACTGCAACCCCGCCCTCTGAATGAACAGGGTCAGCTGCTGCGCTCTGAGAAGCCACAGGTGTGTCAGCT
ATTCCAGAAAGACGGCAGCCTAACAAAGAATATGTGTAAGAACTGCAGAGGAACCTTCTGTAGTGCTGCTTAAGCAAATG
AACTGCCTCTTCCTTCAAGTATCAAGCCTGAGTGAGTTTGCAATCCCTGTCACAAGCATCTGATCCACCAG
ORF - retro_cjac_1829 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.82 % |
| Parental protein coverage: | 70.72 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | GLNVIDANFCMKGEDLDSQVGVIDFSMYLKDG-NSSKGSEGDGQITAIL-DQKNYVEELNRHLNATVNNL |
| GLN..DANFCMKGEDL.SQVGVIDFS.YLKD..NSSKGSEGD.QITAI..DQKNY.EELNR.LNATVNNL | |
| Retrocopy | GLNHTDANFCMKGEDLESQVGVIDFSVYLKDR<NSSKGSEGDSQITAIR<DQKNYLEELNRYLNATVNNL |
| Parental | QAKVDALEKSNTKLT-EELAVANNRIITLQEEMERVK-EESSYILESNRKGPKQDRTAEGQALSEARKHL |
| QAKVDALEKSNTKLT...L.................K.EESSYILESN.KGPKQDRT.EGQALSEARKHL | |
| Retrocopy | QAKVDALEKSNTKLT<RSLKLQTTGLLPYKKKWNKLK<EESSYILESNQKGPKQDRTSEGQALSEARKHL |
| Parental | -KEETQLRLDVEKELEMQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAFKLQSSDLG |
| .K.ETQL.LDVEKELE.QISM.QEMELA.KMLEKDVCEKQDALVSLRQQL.DLR.L.HELAFKLQSSD.G | |
| Retrocopy | >KKETQLQLDVEKELETQISMKQEMELAKKMLEKDVCEKQDALVSLRQQLHDLRDLNHELAFKLQSSD*G |
| Parental | VKQKSELNSRLEEKTNQMAATIKQLEQRLRQAERSRQSAELDNRLFKQDFGDKINSLQLEVEELTRQRNQ |
| VKQKSELNS.LE.....MAATIKQLEQRL.QAERS..SAELD..LFKQDF.DKINSLQL.VE.LTRQ.NQ | |
| Retrocopy | VKQKSELNSLLEN*L--MAATIKQLEQRLHQAERSCKSAELDKQLFKQDFEDKINSLQLKVEDLTRQWNQ |
| Parental | LELELKQEKERRLQNDRSIPGKGSQKPESKMDGKHKMQEENVKLKKSLEESHRLQPHPVDEQDQLLLSEK |
| LELELKQEKE.R.QNDRSIPGKG.QKPESK.DG.HKM.E.N.KLKK.LEE.HRLQP.P..EQ.QLL.SEK | |
| Retrocopy | LELELKQEKE-R*QNDRSIPGKGYQKPESKTDG*HKMLEGNFKLKKPLEERHRLQPRPLNEQGQLLRSEK |
| Parental | PQVCQLCQEDDSLRKNVCQNCRGTFCDACSTNELPLPSSIKPERVCNPCHKHLIKQ |
| PQVCQL.Q.D.SL.KN.C.NCRGTFC.A...NELPLPSSIKPE.VCNPCHKHLI.Q | |
| Retrocopy | PQVCQLFQKDGSLTKNMCKNCRGTFCSAA*ANELPLPSSIKPE*VCNPCHKHLIHQ |
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 |
|---|---|---|
| SRP051959_colon | 0 .00 RPM | 38 .83 RPM |
| SRP051959_heart | 0 .00 RPM | 44 .18 RPM |
| SRP051959_kidney | 0 .00 RPM | 51 .09 RPM |
| SRP051959_liver | 0 .00 RPM | 74 .60 RPM |
| SRP051959_lung | 0 .00 RPM | 49 .21 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 40 .07 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 26 .95 RPM |
| SRP051959_spleen | 0 .04 RPM | 55 .11 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1829 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1829 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1829 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000014529 | 1 retrocopy |
retro_cjac_1829 ,
|
| Nomascus leucogenys | ENSNLEG00000007716 | 1 retrocopy |