RetrogeneDB ID: | retro_cjac_3894 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286112.1:27614..28097(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | COPS7B | ||
| Ensembl ID: | ENSCJAG00000013630 | ||
| Aliases: | None | ||
| Description: | COP9 signalosome subunit 7B [Source:HGNC Symbol;Acc:16760] |
Retrocopy-Parental alignment summary:
>retro_cjac_3894
AGCTTGGCATCAAGAATGAAGTGTATTGCCTACTCTGTGTTGCTGAAAGACCTGGAGATGCAGAATCTTTGGGAACTAGA
AGACCTCATCATTGTGACTGTCTACACTGACATCATCCAGGGCAGCCTGGACCAGCAAAACCAGCTGCTGGAAGTGGATT
TCTGCATTGGCTGTGATATCCGAAAGAATGATATCAATAATATTGTCAAGACCCTGCATGAATTGTGTGACGACTGTGAA
GCAGTTCTGCTGGGCATCGAGCAGCAAGTTCTGAGTGTCAACTAGTACAAAGAAAACCACAACCGAACTCAGCAGCTGGT
AGAAGCAGAGGTAACCAACATCAAGAAGACACTCAAAGCCACCACATCCTCTTCGGCTCAGGAAATGGAGCAGCAGCTGG
CTGAACAGGAGTGTCCTTCTCACGCTGAGCAGAGGCAGCCCACCAAGATGTCTAAAGTGAAAGGTCTGGTCTCCAGCCGC
CAC
ORF - retro_cjac_3894 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.27 % |
| Parental protein coverage: | 61.36 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SLASRMKCIPYSVLLKDLEMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVK |
| SLASRMKCI.YSVLLKDLEM.NL.ELEDLII..VYTDIIQG.LDQ.NQLLEVDFCIG.DIRK.DINNIVK | |
| Retrocopy | SLASRMKCIAYSVLLKDLEMQNLWELEDLIIVTVYTDIIQGSLDQQNQLLEVDFCIGCDIRKNDINNIVK |
| Parental | TLHEWCDGCEAVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAERECPP |
| TLHE.CD.CEAVLLGIEQQVL..N.YKENHNRTQQ.VEAEVTNIKKTLKAT.SSSAQEMEQQLAE.ECP. | |
| Retrocopy | TLHELCDDCEAVLLGIEQQVLSVN*YKENHNRTQQLVEAEVTNIKKTLKATTSSSAQEMEQQLAEQECPS |
| Parental | HAEQRQPTKKMSKVKGLVSSRH |
| HAEQRQPT.KMSKVKGLVSSRH | |
| Retrocopy | HAEQRQPT-KMSKVKGLVSSRH |
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 .27 RPM | 2 .95 RPM |
| SRP051959_heart | 0 .42 RPM | 4 .72 RPM |
| SRP051959_kidney | 0 .13 RPM | 4 .84 RPM |
| SRP051959_liver | 0 .15 RPM | 4 .40 RPM |
| SRP051959_lung | 0 .59 RPM | 5 .86 RPM |
| SRP051959_lymph_node | 0 .94 RPM | 4 .93 RPM |
| SRP051959_skeletal_muscle | 0 .13 RPM | 3 .49 RPM |
| SRP051959_spleen | 0 .50 RPM | 5 .84 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3894 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3894 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3894 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000013630 | 1 retrocopy |
retro_cjac_3894 ,
|
| Oryctolagus cuniculus | ENSOCUG00000016918 | 1 retrocopy | |
| Ochotona princeps | ENSOPRG00000008376 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000009961 | 1 retrocopy |