RetrogeneDB ID: | retro_cjac_3860 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL285268.1:37484..38009(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KITLG | ||
| Ensembl ID: | ENSCJAG00000019661 | ||
| Aliases: | None | ||
| Description: | KIT ligand [Source:HGNC Symbol;Acc:6343] |
Retrocopy-Parental alignment summary:
>retro_cjac_3860
TCTATCATAGACAAACTTGTGAACACATTGGATGACCTTATGGAGTGCGTGGAAGAAAACTCATCTAAGGATCTAAAAAA
ACCATTCAAGAGCCCAGAACCCAGGCTCTTTACTCCTGAAGAATTCTTTAGAATTTTTAATAGATCTTCAGATGCCTTTA
AGGACGTTGTAGTGGCATCTGAAACTAGTGATTGTATGGCTGCTTCAACATTAAGTCCTGAGAAAGAGTCCAGAGTCAGT
GCCACAAAACCATTGATGTTACCCTCTGTTGCAGCCAACTCCCTCAGGAATGACAGCAGTAGCGGTAATAGGAAGGCCAA
AAATCCCCCTGGAGATTCCGGCCTATACTGGGAAGCCATGGCATTGCCAGCCCTCTTTTCTCTTATAATTGGCTTTGCTT
TTGGAGCCTTATACTGGAAAAAGAGACAGCCAAGTCTTACAAGGACAGTTGAAAATACACGAACTAATGAAGAGGATAAT
GAGGTAATTATGCTGCAAGAGAAAGAAAGAGAATTTCAAGAAGTG
ORF - retro_cjac_3860 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.71 % |
| Parental protein coverage: | 64.1 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SIIDKLVNIVDDLVECVKENSSKDLKKPFKSPEPRLFTPEEFFRIFNRSIDAFKDFVVASETSDCMASST |
| SIIDKLVN..DDL.ECV.ENSSKDLKKPFKSPEPRLFTPEEFFRIFNRS.DAFKD.VVASETSDCMA.ST | |
| Retrocopy | SIIDKLVNTLDDLMECVEENSSKDLKKPFKSPEPRLFTPEEFFRIFNRSSDAFKDVVVASETSDCMAAST |
| Parental | LSPEKDSRVSVTKPFMLPSVAANSLRNDSSSSNRKAKNPPGDSGLHWAAMALPALFSLIIGFAFGALYWK |
| LSPEK.SRVS.TKP.MLPSVAANSLRNDSSS.NRKAKNPPGDSGL.W.AMALPALFSLIIGFAFGALYWK | |
| Retrocopy | LSPEKESRVSATKPLMLPSVAANSLRNDSSSGNRKAKNPPGDSGLYWEAMALPALFSLIIGFAFGALYWK |
| Parental | KRQPSLTRTVENIQINEEDNEISMLQEKEREFQEV |
| KRQPSLTRTVEN...NEEDNE..MLQEKEREFQEV | |
| Retrocopy | KRQPSLTRTVENTRTNEEDNEVIMLQEKEREFQEV |
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 | 2 .35 RPM |
| SRP051959_heart | 0 .00 RPM | 4 .82 RPM |
| SRP051959_kidney | 0 .00 RPM | 7 .06 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .19 RPM |
| SRP051959_lung | 0 .00 RPM | 23 .70 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .64 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 5 .70 RPM |
| SRP051959_spleen | 0 .08 RPM | 0 .76 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3860 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3860 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3860 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000019661 | 2 retrocopies |
retro_cjac_3502, retro_cjac_3860 ,
|
| Oryctolagus cuniculus | ENSOCUG00000017687 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000009638 | 1 retrocopy |