RetrogeneDB ID: | retro_cjac_1379 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 15:16368697..16369954(-) | ||
| Located in intron of: | ENSCJAG00000013962 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GRHL2 | ||
| Ensembl ID: | ENSCJAG00000015886 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1379
ATGTCACATGAGTCGGACAATAATAAAAGACTAGTGGCCTTAGTGCCCATGCCCAGTGACCCTCCATTCAATACCCGAAG
AGCCTATACCAGTGAGGATGAAGCCTGGAAGTCATACTTGGAGAATCCCCTGACGGCGGCCACCAAGGCCTTGATGAGCA
TTAATGGTGATGAGGACAGTGCTGCTGCCCTTGGCCTGCTCCATGACTATTACAAGGTTCCTCGAGACAAGAGGCTGCTG
TCTGTAAGCAAAGCAAGTGACAGCCAAGAAGACCAGGAGAAAAGAAACTGCCTTGGCACGAGTGAAGCCCAGAGTAATTT
GAGTGGAGGGGAAAACAGAGTGCAAGTCCTAAAGACTGTTCCAGTGAACCTTTCTCTAAATCAAGATCACCTGGAGAATT
CCAAGCGGGAGCAGTACAGCATCAGCGTCCCCGAGAGCTCTGCCATCATCCCCGTGTCGGGAATCACTGTGGTGAAAGCT
GAAGATTTCACACCAGTTTTCATGACCCCACCTATGCACTATCCCCGGGGAGGTGGGGAAGAACAACGAGTGGTTATCTT
TGAACAGACTCAGTATGACCTGCCCTCGCTGGCCACCCACAGCGCCTATCTCAAGGATGACCAGCGCAGCACCCCAGACA
GCACGTACAGCAAGAGCTTCAAGGACGCAGCCACAGAGAAATTTCGGAGTGCTTCAGTTGGGGCTGAGGAGTACATGTAT
GATCAGACCTCAAGTGGCAGGTTTCAGTATACCCTGGAAGCCACCAAATCTCTCCGCCAGAAGCAGGGGCAGGGCCCCAT
GACCTACCTCAACAAAGGACAGTTCTATGCCATAACACTCAGCGAGACTGCAGACAACAAATGCTTCCGACATCCCATCA
GCAAAGTCAGGAGCGTGGTGATGGTGGTCTTCAGTGAAGACAAGAACAGAGACGAACAGCTCAAATACTGGAAATACTGG
CACTCTCGGCAGCACACAGCGAAGCAGAGGGTCCTTGACATTGCTGATTACAAGGAGAGCTTTAATACAATTGGAAACAT
TGAAGAGATTGCATATAATGCTGTTTCCTTTACCTGGGACGTGAATGAAGAGGCGAAGATTTTCATCACCATGAATTGCT
TGAGTACAGATTTCTCCTCCCAAAAAGGGGTGAAAGGACTGCCTTTGATGATTCAGATTGACACATACAGTTATAACAAT
CGTAGCAATAAACCCATTCATAGAGCTTATTGCCAGATCAAGGTCTTCTGTGACAAA
ORF - retro_cjac_1379 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.37 % |
| Parental protein coverage: | 67.04 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSQESDNNKRLVALVPMPSDPPFNTRRAYTSEDEAWKSYLENPLTAATKAMMSINGDEDSAAALGLLYDY |
| MS.ESDNNKRLVALVPMPSDPPFNTRRAYTSEDEAWKSYLENPLTAATKA.MSINGDEDSAAALGLL.DY | |
| Retrocopy | MSHESDNNKRLVALVPMPSDPPFNTRRAYTSEDEAWKSYLENPLTAATKALMSINGDEDSAAALGLLHDY |
| Parental | YKVPRDKRLLSVSKASDSQEDPEKRNCLGTSEAQSNLSGGENRVQVLKTVPVNLSLNQDHLENSKREQYS |
| YKVPRDKRLLSVSKASDSQED.EKRNCLGTSEAQSNLSGGENRVQVLKTVPVNLSLNQDHLENSKREQYS | |
| Retrocopy | YKVPRDKRLLSVSKASDSQEDQEKRNCLGTSEAQSNLSGGENRVQVLKTVPVNLSLNQDHLENSKREQYS |
| Parental | ISVPESSAIIPVSGITVVKAEDFTPVFMTPPMHYPRGDGEEQRVVIFEQTQYDLPSLAAHSAYLKDDQRS |
| ISVPESSAIIPVSGITVVKAEDFTPVFMTPPMHYPRG.GEEQRVVIFEQTQYDLPSLA.HSAYLKDDQRS | |
| Retrocopy | ISVPESSAIIPVSGITVVKAEDFTPVFMTPPMHYPRGGGEEQRVVIFEQTQYDLPSLATHSAYLKDDQRS |
| Parental | TPDSTYSESFKDAATEKFRSASVGAEEYMYDQTSSGTFQYTLEATKSLRQKQGEGPMTYLNKGQFYAITL |
| TPDSTYS.SFKDAATEKFRSASVGAEEYMYDQTSSG.FQYTLEATKSLRQKQG.GPMTYLNKGQFYAITL | |
| Retrocopy | TPDSTYSKSFKDAATEKFRSASVGAEEYMYDQTSSGRFQYTLEATKSLRQKQGQGPMTYLNKGQFYAITL |
| Parental | SETGDNKCFRHPISKVRSVVMVVFSEDKNRDEQLKYWKYWHSRQHTAKQRVLDIADYKESFNTIGNIEEI |
| SET.DNKCFRHPISKVRSVVMVVFSEDKNRDEQLKYWKYWHSRQHTAKQRVLDIADYKESFNTIGNIEEI | |
| Retrocopy | SETADNKCFRHPISKVRSVVMVVFSEDKNRDEQLKYWKYWHSRQHTAKQRVLDIADYKESFNTIGNIEEI |
| Parental | AYNAVSFTWDVNEEAKIFITVNCLSTDFSSQKGVKGLPLMIQIDTYSYNNRSNKPIHRAYCQIKVFCDK |
| AYNAVSFTWDVNEEAKIFIT.NCLSTDFSSQKGVKGLPLMIQIDTYSYNNRSNKPIHRAYCQIKVFCDK | |
| Retrocopy | AYNAVSFTWDVNEEAKIFITMNCLSTDFSSQKGVKGLPLMIQIDTYSYNNRSNKPIHRAYCQIKVFCDK |
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 | 2 .04 RPM | 14 .29 RPM |
| SRP051959_heart | 0 .84 RPM | 0 .63 RPM |
| SRP051959_kidney | 2 .35 RPM | 12 .85 RPM |
| SRP051959_liver | 0 .50 RPM | 0 .78 RPM |
| SRP051959_lung | 1 .56 RPM | 9 .40 RPM |
| SRP051959_lymph_node | 0 .89 RPM | 0 .55 RPM |
| SRP051959_skeletal_muscle | 0 .81 RPM | 0 .37 RPM |
| SRP051959_spleen | 0 .80 RPM | 0 .48 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1379 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1379 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1379 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 | ENSCJAG00000015886 | 1 retrocopy |
retro_cjac_1379 ,
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