RetrogeneDB ID: | retro_cjac_1680 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 18:28088560..28089187(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TTC33 | ||
| Ensembl ID: | ENSCJAG00000007398 | ||
| Aliases: | None | ||
| Description: | tetratricopeptide repeat domain 33 [Source:HGNC Symbol;Acc:29959] |
Retrocopy-Parental alignment summary:
>retro_cjac_1680
ATTCTTGAATGCCGTGCTGAGAAGAGTAAACAGCTGAAGGATGAAGGAGCCAGTTTGGCTGAAAATAAAAGATACCAGTA
GGCAGTTCAGAAGTGGGATGAAGTACTACAGTTAACTCCAAATCATGCTACCCTATATGAGATGAAATCACAGGTGCTAA
TGTCTCTGCATGAAATGTTCCCAGCAGTACCTGCAGCAGAAATCAGCGTGCAGCAAAATCCACATTCGTGGGAGTCTTGG
CAAACTTTGGGACATGCTCAACTTGGATTAGGAAAGATAATCCTGGCAATTCAAGTAGCCCTTCACATCTATCCAGTGAA
CCCTGAAATATGGAAAGAAGACCTCTCTTGGGCAAGAACACTCCAGGAGCAGCAGAAGGTAGCCCAGATGATTTTAAAAA
AAGTGAAGCACCAGCTGACGTAACACACTTTTCACCCAAGTCAATTCCAGACTATGACTCCAAAAGTGATGAGATTTATT
GCTGTTTGTGCGGCTATTGCTGAGAAACAGAAGACAGTTTCAGCAAATAAAACAATGGTTACTGTGTCCACTTCTGGGGC
CCTAGAGACTGTAACTGAAGAGGAAGATGGTGCTACACCACCAGATGGCTCTGTTTTTGTCAGAGCC
ORF - retro_cjac_1680 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.42 % |
| Parental protein coverage: | 80.84 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ILEGCAEKSKQLKDEGASLAENKRYREAIQKWDEALQLTPNDATLYEMKSQVLMSLHEMFPAVHAAEMAV |
| ILE..AEKSKQLKDEGASLAENKRY..A.QKWDE.LQLTPN.ATLYEMKSQVLMSLHEMFPAV.AAE..V | |
| Retrocopy | ILECRAEKSKQLKDEGASLAENKRYQ*AVQKWDEVLQLTPNHATLYEMKSQVLMSLHEMFPAVPAAEISV |
| Parental | QRNPHSWESWQTLGRAQLGLGEIILAIRSFQVALHIYPMNPEIWKEDLSWARTLQEQQKVAQRIKKSEAP |
| Q.NPHSWESWQTLG.AQLGLG.IILAI...QVALHIYP.NPEIWKEDLSWARTLQEQQKVAQ.I.K.... | |
| Retrocopy | QQNPHSWESWQTLGHAQLGLGKIILAI---QVALHIYPVNPEIWKEDLSWARTLQEQQKVAQMILKKVKH |
| Parental | AEVTH-FLPKSIPDYDFESDEIVAVCAAIAEKEKTVSANKTMVIVSASGAVETVTEKEDGATPPDGSVFI |
| ....H.F.P..............AVCAAIAEK.KTVSANKTMV.VS.SGA.ETVTE.EDGATPPDGSVF. | |
| Retrocopy | QLT*HTFHPSQFQTMTPKVMRFIAVCAAIAEKQKTVSANKTMVTVSTSGALETVTEEEDGATPPDGSVFV |
| Parental | KA |
| .A | |
| Retrocopy | RA |
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 .20 RPM | 23 .85 RPM |
| SRP051959_heart | 0 .14 RPM | 27 .87 RPM |
| SRP051959_kidney | 0 .00 RPM | 30 .84 RPM |
| SRP051959_liver | 0 .19 RPM | 18 .45 RPM |
| SRP051959_lung | 0 .10 RPM | 24 .97 RPM |
| SRP051959_lymph_node | 0 .21 RPM | 27 .05 RPM |
| SRP051959_skeletal_muscle | 0 .04 RPM | 30 .79 RPM |
| SRP051959_spleen | 0 .06 RPM | 28 .07 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1680 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1680 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1680 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 | ENSCJAG00000007398 | 1 retrocopy |
retro_cjac_1680 ,
|
| Otolemur garnettii | ENSOGAG00000011946 | 1 retrocopy |