RetrogeneDB ID: | retro_cjac_1751 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 19:33501572..33502018(-) | ||
| Located in intron of: | ENSCJAG00000016730 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM96A | ||
| Ensembl ID: | ENSCJAG00000004834 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 96, member A [Source:HGNC Symbol;Acc:26235] |
Retrocopy-Parental alignment summary:
>retro_cjac_1751
ATGGAGGGGGCATCTGGGCTGCTCTCCTGGACACAAGCAGAGTCCTGTGGCTCTCAGACCTCTCTGAGCAGGGAGCTGCC
TGGCAGCCCTGGATCATGGAAGAGAAAGTGCTAGAGGTTTATGATTTGATTCAAACTATCCCAGACCCAGAAAAGCCTAA
TATTTTAGAAGAACTGGAATTGGCAATGGAAAGTTGTGTGGAAGTTCAGAAGATAAACGAACAAGACTATGTGGTTATTA
TCAAGGTGACACCACAGTACCGCATTGATATTTGGTGACTCCTATGGAGCTGTGCTTAAAACTTAAGCCATGTTTACCAT
TTAAACATAAGTCGGAAATCTACATTTCTGAAGGAAGCCACTCAACAGAAGAAGACATCAATAAGGGAGATAAATGACAA
AGAAAGAGTGGTGGCTGCAATTGAAAACCCCAACTTAGGGGAAGTG
ORF - retro_cjac_1751 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.43 % |
| Parental protein coverage: | 94.38 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MQRVSGLLSWT-LNRVLWLSGLSEPGAARQLRIMEEKALEVYDLIRTIRDPEKPSTLEELEVVSESCVEV |
| M...SGLLSWT...RVLWLS.LSE.GAA.Q..IMEEK.LEVYDLI.TI.DPEKP..LEELE...ESCVEV | |
| Retrocopy | MEGASGLLSWT<TSRVLWLSDLSEQGAAWQPWIMEEKVLEVYDLIQTIPDPEKPNILEELELAMESCVEV |
| Parental | QEINEEEYLVIIRFTP-TVPHCSLATLIGLCLRVKLQRCLPFKHKLEIYISEGTHSTEEDINK-QINDKE |
| Q.INE..Y.VII..TP.TVPH..L.T...LCL..KL..CLPFKHK.EIYISEG.HSTEEDINK..INDKE | |
| Retrocopy | QKINEQDYVVIIKVTP<TVPH*YLVTPMELCL--KLKPCLPFKHKSEIYISEGSHSTEEDINK>EINDKE |
| Parental | RVAAAMENPNLREI |
| RV.AA.ENPNL.E. | |
| Retrocopy | RVVAAIENPNLGEV |
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 .11 RPM | 7 .61 RPM |
| SRP051959_heart | 0 .09 RPM | 6 .75 RPM |
| SRP051959_kidney | 0 .13 RPM | 8 .30 RPM |
| SRP051959_liver | 0 .02 RPM | 30 .09 RPM |
| SRP051959_lung | 0 .05 RPM | 6 .80 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 10 .32 RPM |
| SRP051959_skeletal_muscle | 0 .09 RPM | 3 .87 RPM |
| SRP051959_spleen | 0 .02 RPM | 14 .52 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1751 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1751 was not experimentally validated.