RetrogeneDB ID: | retro_cjac_2753 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:116180344..116181116(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LUC7L3 | ||
| Ensembl ID: | ENSCJAG00000018558 | ||
| Aliases: | None | ||
| Description: | LUC7-like 3 (S. cerevisiae) [Source:HGNC Symbol;Acc:24309] |
Retrocopy-Parental alignment summary:
>retro_cjac_2753
GTGGTTTCGGCCACATAATTGTTGGATGAGTTAATGGGCTGGGATGGAAACCTCGCCCCAGACAAGAAGCGCAGCAACAT
GTGGTAGGACCACAAGAGCATTTATAAATATTTTCTCTGTGGTTTTTTTCTGCAGAATTGTTCACAAATACACATTCTGA
TCTCGGTCCATGTGAAAAAAACTCATACTGAAAACCTACAAAAGTAGTATAAGAAGAGCTCTTGTTTTATGAAAGTTGGC
TATGAGAGAGGTTTTTCTTTTCCATAATTACAGAGCTTACTTGCAAAAGTAGAGCATAGAATCAGGTGAGGCCATGCTCG
TTTGGCATCTCAAGACCAGCAGTCTTCTTGGGCGGCTGGCCCAACAGGCAAAAATGAAGCAAAAATTCAGGCTCTAACAG
ACAACACTGATGTGCTTCTGCAACAGATTGAAGAATTAGGGGTGGAAGGAAAAGTAGAAGAAGCCCAGTGGAAGATGAAA
TTAGTTGAACAATTAAAAGAAGAGAGAGAATTGCCTAGATCCACAACCTTGAAATTGAAAGTTTTGCTGAACACATACAA
AAAAAATGGAAGTTGGTGAAGTGTGTGGAGCCTTTTTGATAGTAGGAGATGCCCAGTCCCAGGTAGACGACCGTTTGTTG
GGAAGACAACACATGGGATGTGCCAACATTAAAACTACTGTAGAAGAATTAAAAGAAACATTAAGAAAAAGAACTCAAGA
ACTTAATCATGATGACTGTCTAAAAAGGGAAAAGCAAGAAAGAAAAGAGAAA
ORF - retro_cjac_2753 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.48 % |
| Parental protein coverage: | 59.49 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | MISAAQLLDELMGRDRNLAPDEKRSNVRWDHESVCKYYLCGFC-PAELFTNTRSDLGPCEK-IHDENLRK |
| ..SA..LLDELMG.D.NLAPD.KRSN...DH.S..KY.LCGF...AELFTNT.SDLGPCEK..H.ENL.K | |
| Retrocopy | VVSAT*LLDELMGWDGNLAPDKKRSNMW*DHKSIYKYFLCGFF<SAELFTNTHSDLGPCEK>THTENLQK |
| Parental | QYEKSSRFMKVGYERDF-LRYLQSLLAEVERRIRRGHARLALSQNQQSSGAAGPTGKNEEKIQVLTDKID |
| .Y.KSS.FMKVGYER.F....LQSLLA.VE.RIR.GHARLA.SQ.QQSS.AAGPTGKNE.KIQ.LTD..D | |
| Retrocopy | *YKKSSCFMKVGYERGFSFP*LQSLLAKVEHRIR*GHARLA-SQDQQSSWAAGPTGKNEAKIQALTDNTD |
| Parental | VLLQQIEELGSEGKVEEAQGMMKLVEQLKEERELLRSTT-STIESFAAQ-EKQMEVCE-VCGAFLIVGDA |
| VLLQQIEELG.EGKVEEAQ..MKLVEQLKEEREL.RSTT...IESFA....K.......VCGAFLIVGDA | |
| Retrocopy | VLLQQIEELGVEGKVEEAQWKMKLVEQLKEERELPRSTT<LEIESFAEHIQKKWKLVK<VCGAFLIVGDA |
| Parental | QSRVDDHLMGKQHMGYAKIKATVEELKEKLRKRTEEPDRDERLKKEKQEREER |
| QS.VDD.L.G.QHMG.A.IK.TVEELKE.LRKRT.E...D..LK.EKQER.E. | |
| Retrocopy | QSQVDDRLLGRQHMGCANIKTTVEELKETLRKRTQELNHDDCLKREKQERKEK |
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 | 23 .43 RPM |
| SRP051959_heart | 0 .02 RPM | 55 .50 RPM |
| SRP051959_kidney | 0 .00 RPM | 55 .64 RPM |
| SRP051959_liver | 0 .00 RPM | 30 .65 RPM |
| SRP051959_lung | 0 .00 RPM | 83 .31 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 100 .57 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 51 .95 RPM |
| SRP051959_spleen | 0 .00 RPM | 80 .86 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2753 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2753 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2753 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 | ENSCJAG00000018558 | 1 retrocopy |
retro_cjac_2753 ,
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