RetrogeneDB ID: | retro_cjac_1359 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 15:84571556..84572939(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TBL3 | ||
| Ensembl ID: | ENSCJAG00000015245 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1359
GCACTGCAGGATCCGTCGTGCCTGGCTGTGCTGACTGCCCACTACAGCACTGTCACCTCACTGGCTTTCAGTGCCGACGG
CCACACTATGCTCAGCTCCGGCTGTGACAAGATCTGTATCATCTGGGACCTTCAGAGCCACCAGGCCACGAGGACTGTGC
TGGTGTTTGAGAACGTGGAGACCGCTGTGCTGTTGCCAGAGGAGCTGGCATCTGAGCTGGGTATGAAGTCCCCAGGCCTG
CACTTCCTGACAGCTGGCGACCAAGGCACTCTGCGCGTGTGGGAGGCAGCTTCTGGGCAGTGTGTGTACACGCAGGCCCG
GCCGCCGGGCCCTGGGCGGGAGCTGACCCACTGCACCCTGGCCCGCACCGCCGGCCTGCTCCTCAGCGCCACTGCCGACC
ATGACCTGCTGCTCTACGAGGCTCACTCCCCGCGGCTGCAGAAACAGTGCACTGGCTATAGTGAGGAGGTCCTGGATGCC
CGGTTTCTTGGGTCTCAGGACTCCCACATCAGCGTGGCCTCCAATAGCCCCTGCCTGACAGTGTTTGAGCTACAGACATC
AGCCTGCCAGATCCTCCATGGCCACAGGGATATCGTTCTGGCTCTGGACGTGTTCCGGAAGGGGTGGCTCTTTGCCAGCT
GTGCCAAGGATCAGAGTGTCCGAATCTGGAGGATGAACAAGGCTGGCCAGGTGGTCTGCATGACTCAGGGTTCCGGCCAT
ATGCACAGTGTCGGCACCATCTGCTGCTCTAGGCTGAAGGAGCCCTTCCTGGTGACGGGCAGCCAGGACTGCACTGTGAA
GCTGTGGCCTCCTCCCAAAGCCCTGCTGTCTAAGAACACAGCCCCAGACAGTGGCCCTGTCCTCCTGCAGGCCCAGAACA
CTCAGCGTTGCCACGATAAGGATATCAACAGCGTGGCCACTGCCCCCAACGACAAGCTGTTGGCCACGGGCTCATAGGAA
CGCATGGCCAAGCTCTGGGCCCTGTCACAGTGCCAGCTGCTGGGTGTCTTCTCAGGCCACCGGCACGGCCTCTGGTGTGT
CCAGTTCTCTCCCACGGACCAGGTGCCGGCCACAGCCTCAGCTGACGGCACCATCAAGCTCTGGGCGCTCTAGGACTTCA
GCTGTCTCAAGACATTTGAGGGACACGATGCTTCCATGCTGAAGGTGGCCTTTGTGAGCTGGGGCACACAGCTGCTGTCC
AGCGGCTCAGATGGCCTTGTGAAGCTCTGGACCATCAAGAACAACGAGTGTGTGCAGACGCTGGATGCCCACGATGACAA
GGCCTGGGGGCCGCACCACAGCCAGCTGGATGACCGCACCCTCACTGGCGCCAGCGACTCCCAAGTCATCCTCTGGAAGG
ATGTGACCAAGGAGGAGCAGGCC
ORF - retro_cjac_1359 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.94 % |
| Parental protein coverage: | 57.05 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SLQDRSCLAVLTAHYSAVTSLAFSADGHTMLSSGRDKICIIWDLQSHQAVRTVPVFESVETAVLLPEEPA |
| .LQD.SCLAVLTAHYS.VTSLAFSADGHTMLSSG.DKICIIWDLQSHQA.RTV.VFE.VETAVLLPEE.A | |
| Retrocopy | ALQDPSCLAVLTAHYSTVTSLAFSADGHTMLSSGCDKICIIWDLQSHQATRTVLVFENVETAVLLPEELA |
| Parental | SELGVKSPGLHFLTAGDQGTLRVWEAASGQCVYTQARPPGPGRELTHCTLARTAGLLLSATADHNLLLYE |
| SELG.KSPGLHFLTAGDQGTLRVWEAASGQCVYTQARPPGPGRELTHCTLARTAGLLLSATADH.LLLYE | |
| Retrocopy | SELGMKSPGLHFLTAGDQGTLRVWEAASGQCVYTQARPPGPGRELTHCTLARTAGLLLSATADHDLLLYE |
| Parental | ARSLRLQKQFAGYSEEVLDVRFLGPEDSHIIVASNSPCLKVFELQTSACQILHGHTDIVLALDVFRKGWL |
| A.S.RLQKQ..GYSEEVLD.RFLG..DSHI.VASNSPCL.VFELQTSACQILHGH.DIVLALDVFRKGWL | |
| Retrocopy | AHSPRLQKQCTGYSEEVLDARFLGSQDSHISVASNSPCLTVFELQTSACQILHGHRDIVLALDVFRKGWL |
| Parental | FASCAKDQSVRIWRMNKAGQVVCVAQGPGHTHSVGTVCCSRLKESFLVTGSQDCTVKLWPLPKALLSKNT |
| FASCAKDQSVRIWRMNKAGQVVC..QG.GH.HSVGT.CCSRLKE.FLVTGSQDCTVKLWP.PKALLSKNT | |
| Retrocopy | FASCAKDQSVRIWRMNKAGQVVCMTQGSGHMHSVGTICCSRLKEPFLVTGSQDCTVKLWPPPKALLSKNT |
| Parental | APDSGPVLLQPQTNQRCHDKDINSVAIAPNDKLLATGSQDRTAKLWALPQCQLLGVFSGHRRGLWCVQFS |
| APDSGPVLLQ.Q..QRCHDKDINSVA.APNDKLLATGS..R.AKLWAL.QCQLLGVFSGHR.GLWCVQFS | |
| Retrocopy | APDSGPVLLQAQNTQRCHDKDINSVATAPNDKLLATGS*ERMAKLWALSQCQLLGVFSGHRHGLWCVQFS |
| Parental | PMDQVLATASADGTIKLWALQDFSCLKTFEGHDASVLKVAFVSRGTQLLSSGSDGLVKLWTIKNNECVRT |
| P.DQV.ATASADGTIKLWAL.DFSCLKTFEGHDAS.LKVAFVS.GTQLLSSGSDGLVKLWTIKNNECV.T | |
| Retrocopy | PTDQVPATASADGTIKLWAL*DFSCLKTFEGHDASMLKVAFVSWGTQLLSSGSDGLVKLWTIKNNECVQT |
| Parental | LDAHDDKVWGLHCSRLDDCALTGASDSRVILWKDVTEAEQA |
| LDAHDDK.WG.H.S.LDD..LTGASDS.VILWKDVT..EQA | |
| Retrocopy | LDAHDDKAWGPHHSQLDDRTLTGASDSQVILWKDVTKEEQA |
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 | 4 .81 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .42 RPM |
| SRP051959_kidney | 0 .02 RPM | 6 .28 RPM |
| SRP051959_liver | 0 .00 RPM | 4 .77 RPM |
| SRP051959_lung | 0 .00 RPM | 5 .35 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 6 .53 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 9 .96 RPM |
| SRP051959_spleen | 0 .00 RPM | 3 .95 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1359 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1359 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1359 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000015245 | 1 retrocopy |
retro_cjac_1359 ,
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