RetrogeneDB ID: | retro_cjac_1325 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 15:18391042..18392036(+) | ||
| Located in intron of: | ENSCJAG00000001685 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RACGAP1 | ||
| Ensembl ID: | ENSCJAG00000021058 | ||
| Aliases: | None | ||
| Description: | Rac GTPase activating protein 1 [Source:HGNC Symbol;Acc:9804] |
Retrocopy-Parental alignment summary:
>retro_cjac_1325
GTTCCACGTGGAAAGCAGATAAAATTTGGCAAACTATCTCTGAAGCGTCAAGACTGTCATGTGGTCTCTCATCCAGAATG
TCGGGACCGCTTTCCCATTCCCTGCATTCCTACCCTGATAGGAACACCTGTCAAGATTGGAGAGGGAATGCTGGCAGACT
TTGTGTCCCAGACTTCTCCAATGATCCTCTCCATTGTTGTGATGGTGTTAATGAGATTGAGCAGAGAGGTCTGACTGAGA
CAGGCCTGTATAGGATCTCTGGCTGTGACTGCACAGTAAAAGAGCTGAAAGAGAAATTCCTCAGAGTGAAAACTGTACCC
TTCCTCAGCAAAGTGGATGATATCCATGCTATCTGTAGCCTTCTAAAAGACTTTCTTTGAAACCTCAAAGAACCTCTTCT
GACCTTTCGCCTAAACAAAGCCTTTATGGAAGCAGCAGAAATCACAGATGAAGACAACAGCATAGCTGCCATGTACCAGG
CTGTTGGTGAACTGCCCCAGGCCAACAGGGACACATTAGCTTTCCTCATGATTCACTTGTAACAGTGGCACAGAGTCCAC
ATACTAAAATGGATTTTGCCAATCTGGCTAAAGTTTTTAGCCCTACAATAGTGGCCCATGCTGTGCCCAATCCAGACCCA
GTGACAATGTTACAGGACATCAAGCGTCAACCCAAGGTGGTTGAGCGCCTGCTTTCCTTGTCCCTGGAGTATTGGAGTCA
GTTCATGATGGTAGAACAACAGAACACTGACCCCCTACATGTCATTGAAAACTCAAATGCCTTTTCAACGCCACAGACAC
CAGATATTCAAGTGAGTTTACAGGGACCTGTGACCACTCCTGAACATCAGCTTCTCAAGACTCCTTCATCTAGTTCTCTG
TCACAGAGAGTTCGTTCCACCCTCACCAAGAACACTCCCAGATTTAGGAGCAAAAGCAAGTCTGCCACCAACCTAGGATG
ACAAGGCAAATTTTTTGCTTCTCCAATGCTCAAG
ORF - retro_cjac_1325 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.22 % |
| Parental protein coverage: | 52.04 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VPFDVLIKIQAXSLKCRDCRVVSHPECRDRCP-PCNPTLIGTPVKIGEGMLADFVSQTSPMIPSIVVHC- |
| VP....IK....SLK..DC.VVSHPECRDR.P.PC.PTLIGTPVKIGEGMLADFVSQTSPMI.SIVV... | |
| Retrocopy | VPRGKQIKFGKLSLKRQDCHVVSHPECRDRFPIPCIPTLIGTPVKIGEGMLADFVSQTSPMILSIVVMV< |
| Parental | VNEIEQRGLTETGLYRISGCDRTVKELKEKFLRVKTVPLLSKVDDIHAICSLLKDFLRNLKEPLLTFRLN |
| VNEIEQRGLTETGLYRISGCD.TVKELKEKFLRVKTVP.LSKVDDIHAICSLLKDFL.NLKEPLLTFRLN | |
| Retrocopy | VNEIEQRGLTETGLYRISGCDCTVKELKEKFLRVKTVPFLSKVDDIHAICSLLKDFL*NLKEPLLTFRLN |
| Parental | KAFMEAAEIADEDNSIAAMYQAVGELPQANRDTLAFLMIHMQR-VAQSPHTKMDVANLAKVFGPTIVAHA |
| KAFMEAAEI.DEDNSIAAMYQAVGELPQANRDTLAFLMIH....VAQSPHTKMD.ANLAKVF.PTIVAHA | |
| Retrocopy | KAFMEAAEITDEDNSIAAMYQAVGELPQANRDTLAFLMIHL*Q<VAQSPHTKMDFANLAKVFSPTIVAHA |
| Parental | VPNPDPVTMLQDIKRQPKVVERLLSLPLEYWSQFMMVEQENIDPLHVIENSNAFSTPQTPDIKVSLLGPV |
| VPNPDPVTMLQDIKRQPKVVERLLSL.LEYWSQFMMVEQ.N.DPLHVIENSNAFSTPQTPDI.VSL.GPV | |
| Retrocopy | VPNPDPVTMLQDIKRQPKVVERLLSLSLEYWSQFMMVEQQNTDPLHVIENSNAFSTPQTPDIQVSLQGPV |
| Parental | TTPEHQLLKTPSSSSLSQRVRSTLTKNTPRFGSKSKSATNLGRQGNFFASPMLK |
| TTPEHQLLKTPSSSSLSQRVRSTLTKNTPRF.SKSKSATNLG.QG.FFASPMLK | |
| Retrocopy | TTPEHQLLKTPSSSSLSQRVRSTLTKNTPRFRSKSKSATNLG*QGKFFASPMLK |
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 .67 RPM | 19 .28 RPM |
| SRP051959_heart | 0 .28 RPM | 2 .32 RPM |
| SRP051959_kidney | 0 .31 RPM | 2 .53 RPM |
| SRP051959_liver | 0 .19 RPM | 1 .49 RPM |
| SRP051959_lung | 0 .23 RPM | 8 .83 RPM |
| SRP051959_lymph_node | 0 .82 RPM | 17 .05 RPM |
| SRP051959_skeletal_muscle | 0 .13 RPM | 1 .59 RPM |
| SRP051959_spleen | 0 .36 RPM | 9 .94 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1325 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1325 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1325 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000001701 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000021058 | 2 retrocopies |
retro_cjac_1325 , retro_cjac_837,
|