RetrogeneDB ID: | retro_cjac_2150 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:75345334..75345714(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KRBOX1 | ||
| Ensembl ID: | ENSCJAG00000031316 | ||
| Aliases: | ZNF662, KRBOX1 | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2150
ATGACAACTATGTCCTCAACAGCCAGGCCTCAGGAATCGGTGGCTTTTGAGGACGTGGCTGTATACTTCACTAAGAAGGA
ACGGGCCATCTTGGTGCCTGACCAGAGGCCTTGTACTGTGTGATGCTGGAAAACTATGAGGCCGTGGCCTTTGTAGCAGT
GCTACCCACTTCCAAACTAGCTTCTGTCTCTCATCTGGAGCAAGGGAAAGAGCCCTGTTTCACCCAACTACAGGGAGTCC
TAAGCAGGAGGGGCTGGAGAGCAGGCTTTATAGGATATTTGGAACTGAGAAGATACACTTACTTAGCTAAAGCAATGTTA
TGTATAATAAAATCAAAAATTCTTCAAAATCATCAGTGCTGTGAAGACAGGAGAAAGAGT
ORF - retro_cjac_2150 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.95 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MTTVSSTARPQESVAFDDVAVYFTKKEWAIMVPDQR-ALYRDVMLENYEAVAFV-VPPTSKPALISHLEQ |
| MTT.SSTARPQESVAF.DVAVYFTKKE.AI.VPDQR.ALY..VMLENYEAVAFV.V.PTSK.A..SHLEQ | |
| Retrocopy | MTTMSSTARPQESVAFEDVAVYFTKKERAILVPDQR<ALYC-VMLENYEAVAFVAVLPTSKLASVSHLEQ |
| Parental | GKEPCFTQPQGVLSRRDWRAGFIGHSELRRYTYLAKAMLYVIKSKILQNRRCWEDRRKA |
| GKEPCFTQ.QGVLSRR.WRAGFIG..ELRRYTYLAKAML..IKSKILQN..C.EDRRK. | |
| Retrocopy | GKEPCFTQLQGVLSRRGWRAGFIGYLELRRYTYLAKAMLCIIKSKILQNHQCCEDRRKS |
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 | 3 .11 RPM |
| SRP051959_heart | 0 .04 RPM | 3 .53 RPM |
| SRP051959_kidney | 0 .00 RPM | 6 .88 RPM |
| SRP051959_liver | 0 .09 RPM | 7 .67 RPM |
| SRP051959_lung | 0 .00 RPM | 2 .38 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .80 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 9 .19 RPM |
| SRP051959_spleen | 0 .02 RPM | 1 .37 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2150 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2150 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2150 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000031316 | 3 retrocopies |
retro_cjac_2150 , retro_cjac_2724, retro_cjac_2790,
|