RetrogeneDB ID: | retro_cjac_687 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 10:55227081..55227383(+) | ||
| Located in intron of: | ENSCJAG00000005822 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | IFT20 | ||
| Ensembl ID: | ENSCJAG00000012534 | ||
| Aliases: | None | ||
| Description: | intraflagellar transport 20 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:30989] |
Retrocopy-Parental alignment summary:
>retro_cjac_687
ATGGCCAAGGACATCCTGGGTGAAGCAGGGCTGCATTTTGATGAGCTGAACAAGCTGCAGGTGTTGGACCCAGAGGTTAC
CCAGCAGACCACAGTGCTCAAAGAGTATACAAAATTGTGGACAAAATTGGCCAATTTCAGAAAATAGTTGGTTTAATTGA
GCTTGTTGATCAACTTGCAAAAGCAGCAGAAAATGAGAAGATGAAGGCCAATGGTGCTCAGAACTTGCTCAAATTAACAG
CAAAGTAGAGAGAAGCTCAACAACTTCAGAACTCAGCTTTAAGTACTGACAGAAAAAAAGAA
ORF - retro_cjac_687 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.15 % |
| Parental protein coverage: | 78.03 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAKDILGEAGLHFDELNKLRVLDPEVTQQTIELKEECKDFVDKIGQF-QKIVGGLIELIDQLAKEAENEK |
| MAKDILGEAGLHFDELNKL.VLDPEVTQQT..LKE..K....K...F.QKIV.GLIEL.DQLAK.AENEK | |
| Retrocopy | MAKDILGEAGLHFDELNKLQVLDPEVTQQTTVLKEYTKLWT-KLANF<QKIV-GLIELVDQLAKAAENEK |
| Parental | MKAIGARNLLKSIAKQREAQQQQLQALIAEKKMQ |
| MKA.GA.NLLK..AK.REAQQ.Q..AL....K.. | |
| Retrocopy | MKANGAQNLLKLTAK*REAQQLQNSALSTDRKKE |
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 | 5 .08 RPM |
| SRP051959_heart | 0 .46 RPM | 5 .47 RPM |
| SRP051959_kidney | 0 .22 RPM | 8 .12 RPM |
| SRP051959_liver | 0 .13 RPM | 10 .14 RPM |
| SRP051959_lung | 0 .20 RPM | 7 .79 RPM |
| SRP051959_lymph_node | 0 .43 RPM | 7 .15 RPM |
| SRP051959_skeletal_muscle | 0 .85 RPM | 2 .71 RPM |
| SRP051959_spleen | 0 .32 RPM | 7 .25 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_687 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_687 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_687 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1314 |
| Gorilla gorilla | retro_ggor_1026 |
| Pongo abelii | retro_pabe_1097 |
| Macaca mulatta | retro_mmul_2165 |