RetrogeneDB ID: | retro_cjac_1077 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 13:27937179..27937771(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SCD | ||
| Ensembl ID: | ENSCJAG00000017338 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1077
AAGTTTTCAGAAACAGATGCTGATCCTCATAATTCCCGACGTGGCTTTTTCTTCTCTCACATGGGCTGGCTGCTTGTGCC
CAAACACCCAGGTGTCAAAGAGAAGGGCGGTACACTGGACTTGTCTGACCTAAAAGCTGAGAAACTGGTGATGTTCCAGA
GGAGGTACTACAAACCTGGCATGCTGCTGATGTGCTTCATCCTGCCCACACTTGTGCCCTTTTATTTCTGGGGTGAAACT
TTTCAACACAGCTTGTACGTTGCCACTTTCTTGCGATATGCTGTAGTGCTTAATGCCACCTGGCTGGTGAACAGCGCTGC
CCACCTCTACAGATATCGTCCTTACGACAAGAACATTAGCCCCCGGGAGAACGTCCTGCTTTCGCTTGGAGCTGTGGGTG
AAGGCTTCCACAACTCACCACTCCTTTCCCTATGACTACTCTGCCAGTGAGTACCGCTGGCACATCAACGTAACCACATT
CTTCATTGATTGCATGGCTGCCCTCGGTCTGGCCTATGACCAGAAGAAAGTCTCCAAGGCCGCCATCTTGGCCAGGATTA
AAACAATTGGGGGTGGAAGCTACAAAAGTGGC
ORF - retro_cjac_1077 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.46 % |
| Parental protein coverage: | 55.15 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | KFSETDADPHNSRRGFFFSHVGWLLVRKHPAVKEKGGTLDLSDLKAEKLVMFQRRYYKPGVLLMCFILPT |
| KFSETDADPHNSRRGFFFSH.GWLLV.KHP.VKEKGGTLDLSDLKAEKLVMFQRRYYKPG.LLMCFILPT | |
| Retrocopy | KFSETDADPHNSRRGFFFSHMGWLLVPKHPGVKEKGGTLDLSDLKAEKLVMFQRRYYKPGMLLMCFILPT |
| Parental | LVPFYFWGETFQHSLYVATFLRYAVVLNATWLVNSAAHLYGYRPYDKNISPRENILVSFGAVGEGFHN-Y |
| LVPFYFWGETFQHSLYVATFLRYAVVLNATWLVNSAAHLY.YRPYDKNISPREN.L.S.GAVGEGFHN.. | |
| Retrocopy | LVPFYFWGETFQHSLYVATFLRYAVVLNATWLVNSAAHLYRYRPYDKNISPRENVLLSLGAVGEGFHN>H |
| Parental | HHSFPYDYSASEYRWHINLTTFFIDCMALLGLAYDRKKVSKAAILARIKRTGDGSYKSG |
| H.SFPYDYSASEYRWHIN.TTFFIDCMA.LGLAYD.KKVSKAAILARIK..G.GSYKSG | |
| Retrocopy | H-SFPYDYSASEYRWHINVTTFFIDCMAALGLAYDQKKVSKAAILARIKTIGGGSYKSG |
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 | 29 .60 RPM |
| SRP051959_heart | 0 .00 RPM | 126 .52 RPM |
| SRP051959_kidney | 0 .00 RPM | 22 .14 RPM |
| SRP051959_liver | 0 .24 RPM | 2504 .81 RPM |
| SRP051959_lung | 0 .00 RPM | 49 .47 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 4 .09 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 41 .34 RPM |
| SRP051959_spleen | 0 .00 RPM | 12 .27 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1077 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1077 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1077 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000017338 | 2 retrocopies |
retro_cjac_1077 , retro_cjac_2348,
|
| Homo sapiens | ENSG00000099194 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000010817 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000002566 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000002847 | 1 retrocopy | |
| Drosophila melanogaster | FBgn0086687 | 1 retrocopy |