RetrogeneDB ID: | retro_cjac_3968 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286450.1:451456..451925(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HHEX | ||
| Ensembl ID: | ENSCJAG00000008627 | ||
| Aliases: | None | ||
| Description: | hematopoietically expressed homeobox [Source:HGNC Symbol;Acc:4901] |
Retrocopy-Parental alignment summary:
>retro_cjac_3968
CATGCCCTGCTCTGCCATGACCCCCTGCAGAAACCTCTACTTTGGAGCTCCTTCTTGCAGAAGTCTCTGCATAAAAGGAA
AGGAGGCCAGGTGAGGTTCTCCAACGACCAGACCATCAAGCTGGAGAAGTTCGAGATGCAGAAATACCTCTCTCTGCCCG
AGAGAAAGCATCTGGCCAAGATGCTGCAGCTTAGCAAGAGACAGGTCAAAACCTGGTTTAAGAATCGACATGCTAAATGG
AGGAGACTAAAACAGGAGAACCCTCAAAGCAATAAAAAATGAAGAACTGGAAAGTTTGGACAATTCCTGTGACCAGAGGC
AAGATTTGCCCAGTGAACAGAATAAATGTGCTTCTTTAGATAGCTCTCAGTGTTCGCCCTCCCCTGCCTCTTAGGAAGAC
CTTGATTCAGAGATTTCAGAGGATTCGGATCAGGAAGTGGACATTGAGGGTGATAAAGGATATTTTAAT
ORF - retro_cjac_3968 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.24 % |
| Parental protein coverage: | 58.15 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | HALLRHDPLGKPLLWSPFLQRPLHKRKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQV |
| HALL.HDPL.KPLLWS.FLQ..LHKRKGGQVRFSNDQTI.LEK.FE.QKYLS.PERK.LAKMLQLS.RQV | |
| Retrocopy | HALLCHDPLQKPLLWSSFLQKSLHKRKGGQVRFSNDQTIKLEK-FEMQKYLSLPERKHLAKMLQLSKRQV |
| Parental | KTWFQNRRAKWRRLKQENPQSNKK-EELESLDNSCDQRQDLPSEQNKGASLDSSQCSPSPASQEDLESEI |
| KTWF.NR.AKWRRLKQENPQSNKK.EELESLDNSCDQRQDLPSEQNK.ASLDSSQCSPSPAS.EDL.SEI | |
| Retrocopy | KTWFKNRHAKWRRLKQENPQSNKK>EELESLDNSCDQRQDLPSEQNKCASLDSSQCSPSPAS*EDLDSEI |
| Parental | SEDSDQEVDIEGDKGYFN |
| SEDSDQEVDIEGDKGYFN | |
| Retrocopy | SEDSDQEVDIEGDKGYFN |
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 | 1 .13 RPM |
| SRP051959_heart | 0 .00 RPM | 3 .03 RPM |
| SRP051959_kidney | 0 .00 RPM | 1 .46 RPM |
| SRP051959_liver | 0 .00 RPM | 21 .47 RPM |
| SRP051959_lung | 0 .00 RPM | 7 .56 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .05 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .57 RPM |
| SRP051959_spleen | 0 .00 RPM | 9 .52 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3968 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3968 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3968 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 | ENSCJAG00000008627 | 1 retrocopy |
retro_cjac_3968 ,
|
| Sus scrofa | ENSSSCG00000010472 | 1 retrocopy |