RetrogeneDB ID: | retro_cjac_1627 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 18:6598313..6598865(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | C6orf58 | ||
| Ensembl ID: | ENSCJAG00000003611 | ||
| Aliases: | None | ||
| Description: | chromosome 6 open reading frame 58 [Source:HGNC Symbol;Acc:20960] |
Retrocopy-Parental alignment summary:
>retro_cjac_1627
GTACTTGGGATATCATCAGACCAAGTCAGTCTTTTGCCCCCACCCAAGAATCAGAGCAAGTTTTGGTATAATGTTTCTAG
CTGTCATTCATCCTTCCCTGAGACAATGAGCAAGTGGAACACCTTTTACCAGCATGTGCAGTCACCTTTTAGTAAGTTTG
ATGATCTGTTGAAGTACTTATGGACTGAACATACTTCAACCCTGGCAGATACTATCAAAAGCTTTGAAGACAGATATGAG
TATTATTCTAAAACAGAAGCACATTTTGAGAGAAGTTGGGTAGTGGCTGTGGAATACATAGCTGCGGTCCACTTTCCCAC
AACCTTGATTAGAAAAAAATGTAACTCCCAGAAGGGCCTGCCACCACGAATTCTTGCTACTACTGATGTAGGCCCTTTCA
TCAGTGACTGTACTGCTTTTCAGAATGTAGTCCTGCTTCTTCTAAATATGCTTGGCAACATGGATACATCTACAGGTTAG
CTTTGTACAGGAAAACCTGATGGATATAGCGGTCACTTGGAATCTAGCTGTAGAGATTATGGAAAGAACTCC
GTACTTGGGATATCATCAGACCAAGTCAGTCTTTTGCCCCCACCCAAGAATCAGAGCAAGTTTTGGTATAATGTTTCTAG
CTGTCATTCATCCTTCCCTGAGACAATGAGCAAGTGGAACACCTTTTACCAGCATGTGCAGTCACCTTTTAGTAAGTTTG
ATGATCTGTTGAAGTACTTATGGACTGAACATACTTCAACCCTGGCAGATACTATCAAAAGCTTTGAAGACAGATATGAG
TATTATTCTAAAACAGAAGCACATTTTGAGAGAAGTTGGGTAGTGGCTGTGGAATACATAGCTGCGGTCCACTTTCCCAC
AACCTTGATTAGAAAAAAATGTAACTCCCAGAAGGGCCTGCCACCACGAATTCTTGCTACTACTGATGTAGGCCCTTTCA
TCAGTGACTGTACTGCTTTTCAGAATGTAGTCCTGCTTCTTCTAAATATGCTTGGCAACATGGATACATCTACAGGTTAG
CTTTGTACAGGAAAACCTGATGGATATAGCGGTCACTTGGAATCTAGCTGTAGAGATTATGGAAAGAACTCC
ORF - retro_cjac_1627 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.87 % |
| Parental protein coverage: | 55.45 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | IMGISSDQVNLLPPPKNQRKFCYNVSSCHSSFPETMSKWNIFYQHLQSPFSKFDDLLKYLWTAHTSTLAD |
| ..GISSDQV.LLPPPKNQ.KF.YNVSSCHSSFPETMSKWN.FYQH.QSPFSKFDDLLKYLWT.HTSTLAD | |
| Retrocopy | VLGISSDQVSLLPPPKNQSKFWYNVSSCHSSFPETMSKWNTFYQHVQSPFSKFDDLLKYLWTEHTSTLAD |
| Parental | TIKSFEDRYDYYSKTEAHFERSWVVAVEYIAAVHFPTTLIR-TYNFQKGLPPRILVTTDVAPFINDFTTF |
| TIKSFEDRY.YYSKTEAHFERSWVVAVEYIAAVHFPTTLIR...N.QKGLPPRIL.TTDV.PFI.D.T.F | |
| Retrocopy | TIKSFEDRYEYYSKTEAHFERSWVVAVEYIAAVHFPTTLIRKKCNSQKGLPPRILATTDVGPFISDCTAF |
| Parental | QNVVLLLLNMLGNMDKSTGYLCTEKPNEYSSHLESSSRDYGNNS |
| QNVVLLLLNMLGNMD.STG.LCT.KP..YS.HLESS.RDYG.NS | |
| Retrocopy | QNVVLLLLNMLGNMDTSTG*LCTGKPDGYSGHLESSCRDYGKNS |
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 | 0 .02 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .00 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .07 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .19 RPM |
| SRP051959_lung | 0 .02 RPM | 1 .46 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 3 .08 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .02 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .86 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1627 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1627 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1627 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 | ENSCJAG00000003611 | 1 retrocopy |
retro_cjac_1627 ,
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