RetrogeneDB ID: | retro_cjac_2148 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:74287665..74288268(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | COPS4 | ||
| Ensembl ID: | ENSCJAG00000005067 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2148
AAAAACTACTATGTAGATTATAAACTGGAGATTTACTTGAAGATTGCTAGGCTATATCTGGAGGATGATAATCCAGTCCA
GGCGGAGGCTTACATAAATAGAGGATTGTTGCTTCAGAATGAATCAACCAATGAACAGTTACAGATACATTATAAGGTAT
GCTATGTATGTGTTCTTGATTATAGAAGAAAATTCACTGAAGCTGCGCAAAGGTACAATGAGCTCTCTTACAAGACAATA
GTCCATGAAAGTGAAAGACTAGAGGTCTTAAAACATGGTTTGCACTGTACCATCTTAGCATCAGCAGGACAGCAGCATTC
TTGAATGCTAGCTACTCTTTTTAAGGATGAAAGCTGCCAGCAACTTGCTGCCTATGGGATCCTAGAGAAAATGTACCTGG
ATAGGATCATCAGAGGAAATCAGCTTCAAGAATTTGCTGCCATGCTGATGCCTCACCAAAAAGCAACTACAGCTGATGGT
TCCAGCATCTTGGACAGAGCTGTTATTGAACACAATTTGTTGTCTGCAAGTAAATTATATAATAATATTACCTTCGAAGA
ACTTGGAGCTCTTTTAGAGATTCCTTCGGCTAAGGCAGAAAAG
ORF - retro_cjac_2148 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.04 % |
| Parental protein coverage: | 57.1 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTNEQLQIHYKVCYARVLDYRRKFIEAAQ |
| K.Y.VDYKLE.YLKIARLYLEDD.PVQAEAYINR..LLQNESTNEQLQIHYKVCY..VLDYRRKF.EAAQ | |
| Retrocopy | KNYYVDYKLEIYLKIARLYLEDDNPVQAEAYINRGLLLQNESTNEQLQIHYKVCYVCVLDYRRKFTEAAQ |
| Parental | RYNELSYKTIVHESERLEALKHALHCTILASAGQQRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGN |
| RYNELSYKTIVHESERLE.LKH.LHCTILASAGQQ.S.MLATLFKDE.CQQLAAYGILEKMYLDRIIRGN | |
| Retrocopy | RYNELSYKTIVHESERLEVLKHGLHCTILASAGQQHS*MLATLFKDESCQQLAAYGILEKMYLDRIIRGN |
| Parental | QLQEFAAMLMPHQKATTADGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKHEK |
| QLQEFAAMLMPHQKATTADGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIP.AK.EK | |
| Retrocopy | QLQEFAAMLMPHQKATTADGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIPSAKAEK |
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 | 1 .33 RPM | 13 .51 RPM |
| SRP051959_heart | 2 .02 RPM | 15 .52 RPM |
| SRP051959_kidney | 2 .46 RPM | 15 .86 RPM |
| SRP051959_liver | 1 .45 RPM | 11 .81 RPM |
| SRP051959_lung | 1 .68 RPM | 12 .17 RPM |
| SRP051959_lymph_node | 1 .48 RPM | 14 .36 RPM |
| SRP051959_skeletal_muscle | 2 .80 RPM | 21 .12 RPM |
| SRP051959_spleen | 2 .16 RPM | 14 .60 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2148 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2148 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2148 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000005067 | 2 retrocopies |
retro_cjac_2148 , retro_cjac_2345,
|
| Monodelphis domestica | ENSMODG00000019311 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000017599 | 2 retrocopies |