RetrogeneDB ID: | retro_cjac_2451 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:75086723..75087146(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SLC25A17 | ||
| Ensembl ID: | ENSCJAG00000004636 | ||
| Aliases: | None | ||
| Description: | solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kDa), member 17 [Source:HGNC Symbol;Acc:10987] |
Retrocopy-Parental alignment summary:
>retro_cjac_2451
ACAGTGCTTTTTCCCCTGGATACAGCTAGACTTCGACTTCAGGTTGACGAGAAAAGAAAATACAAAATTACACACATGGT
GCTCCTGGAGATCATTAAAAAGAAGGACTCTTGGCACTATATCGAGGGTGGTTTCCAGCGATTCTCAGTCTCTGCTGCTC
CAATTTTGTCTATTCCTACACTTCTAAAAGCCTCAAAGCAGTCTGGGTCAAAGGTCAACGTTCTACTACTGGAAAAGATC
TGGTAGTTGCTGTTTGTTGCAGGCGTGGTTAACACGTGGCTAACAACTCCACTCTGGGTGGTAAACACCAGAATGAAGCT
TCAAGGGGCAAAATTTAGGACTGAAGATTATACCGACAAACTACAAAGGTATCATGGATGCTTTGTATCAGATCATTCGA
GGTGAAGAAATCTTGGCTTGTTG
ORF - retro_cjac_2451 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.13 % |
| Parental protein coverage: | 53.67 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | TVFFPLDTARLRLQVDEKRKSKTTHMVLLEIIKE-EGLLAPYRGWFPVISSLCCSNFVYFYTFNSLKAVW |
| TV.FPLDTARLRLQVDEKRK.K.THMVLLEIIK..EGLLA.YRGWFP.I.SLCCSNFVY.YT..SLKAVW | |
| Retrocopy | TVLFPLDTARLRLQVDEKRKYKITHMVLLEIIKK<EGLLALYRGWFPAILSLCCSNFVYSYTSKSLKAVW |
| Parental | VKGQRSTTGKDLVIG-FVAGVVNVLLTTPLWVVNTRLKLQGAKFRNEDIVP--TNYKGIIDAFHQIIRDE |
| VKGQRSTTGKDLV...FVAGVVN..LTTPLWVVNTR.KLQGAKFR.ED.......Y.G.....H...R.. | |
| Retrocopy | VKGQRSTTGKDLVVA>FVAGVVNTWLTTPLWVVNTRMKLQGAKFRTEDYTDKLQRYHGCFVSDHSR*RNL |
| Parental | GIL |
| G.L | |
| Retrocopy | GLL |
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 .53 RPM |
| SRP051959_heart | 0 .02 RPM | 3 .53 RPM |
| SRP051959_kidney | 0 .00 RPM | 6 .48 RPM |
| SRP051959_liver | 0 .00 RPM | 4 .05 RPM |
| SRP051959_lung | 0 .00 RPM | 4 .25 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 3 .38 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .92 RPM |
| SRP051959_spleen | 0 .00 RPM | 3 .24 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2451 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2451 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2451 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000004636 | 1 retrocopy |
retro_cjac_2451 ,
|
| Macaca mulatta | ENSMMUG00000008106 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000013036 | 1 retrocopy |