RetrogeneDB ID: | retro_cjac_837 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 11:23559799..23560800(+) | ||
| Located in intron of: | None | ||
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_837
TCCTATGTTCCATGTGGAAAGTGGATAAAATTCAGCAAACTATCTCTGAAGTGTCGAGACTGTTGTGTGGTGTCTCATCC
AGGATGTTGGGACCGCTGTCCCGTTCCCTTCATTTCTACCCTGATAGGAACACCTGTCAAGACTGGAGAGAGAATGCTGG
CAGATTTTGTGTCCCAGACTTCTCCAATGATCCCCCGCCACTGGTGTGCATTGTGTAAATGAGAGTGAGCAGAGATGTGA
CTGAGACAGGCCCGTATAGGATCTCTGGCTGTGACTGCACAGTAAAAGAGCCGAAAGAGAAATTCCTCAGAGTGAAAACT
GTACCCCTCCTCAGCAAAGTAGATGGTATCTTTGTGATCTGTAGCCTTCTGAAAGACTTTCTTCAAAACCTCAAAGAACC
TCTTCTGACCTTTCGCCTAAACAAAGCCTTTATGGAGGCAGCAGAAATCACAGATGAAGTCAATAGCATAGCTGCCAAGT
ACCAGGGTGTTGGTGAACTGCCCCAGGCCAACAGGGACACATTAGCTTTCCTCATGATTCACTTGCAGAGAGTGGTTCAG
AGTCCACATACTAAAATGGATGTTGCCAATCTGGCTATAATCTTTGGCTCTACAATAGTGGCCCATGCTGTGCCCAATCC
AGACCCAGTGACAATGTTACAGGACATCAAGTGTCAACCCAAGGTAGTTGAGCACCTGCTTTCCTTGTCCCTGGAGTATT
GGAATCAGTTCATCATGATGGAACAAGAGAACATTGACGCCCTACATGTCATCGAAAACTCAAATGCCTTTTCAACACCA
CAAACACCAGATATTAAAGTGAGTTTACTGGGACCTGTGACCACTCCCAAATGTCAGCTTCTCAAGACTCCTTCATCTGG
TTCCCTGTCATAGAGAATTCATTCTACCCTCAACAAGAACACTCCCAGATTTGGGCGCAAAAGCAAGTCTGCCACCAACC
TAGGATGACAAGGCAACTTTTTTGCTTCTCCAATGCTCAAG
ORF - retro_cjac_837 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.9 % |
| Parental protein coverage: | 52.36 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AFVPFDVLIKIQAXSLKCRDCRVVSHPECRDRCP-PCNPTLIGTPVKIGEGMLADFVSQTSPMI-PSIVV |
| ..VP....IK....SLKCRDC.VVSHP.C.DRCP.P...TLIGTPVK.GE.MLADFVSQTSPMI.P...V | |
| Retrocopy | SYVPCGKWIKFSKLSLKCRDCCVVSHPGCWDRCPVPFISTLIGTPVKTGERMLADFVSQTSPMI<PPPLV |
| Parental | HCVNEIEQRGLTETGLYRISGCDRTVKELKEKFLRVKTVPLLSKVDDIHAICSLLKDFLRNLKEPLLTFR |
| ..V.....R..TETG.YRISGCD.TVKE.KEKFLRVKTVPLLSKVD.I..ICSLLKDFL.NLKEPLLTFR | |
| Retrocopy | CIV*MRVSRDVTETGPYRISGCDCTVKEPKEKFLRVKTVPLLSKVDGIFVICSLLKDFLQNLKEPLLTFR |
| Parental | LNKAFMEAAEIADEDNSIAAMYQAVGELPQANRDTLAFLMIHMQRVAQSPHTKMDVANLAKVFGPTIVAH |
| LNKAFMEAAEI.DE.NSIAA.YQ.VGELPQANRDTLAFLMIH.QRV.QSPHTKMDVANLA..FG.TIVAH | |
| Retrocopy | LNKAFMEAAEITDEVNSIAAKYQGVGELPQANRDTLAFLMIHLQRVVQSPHTKMDVANLAIIFGSTIVAH |
| Parental | AVPNPDPVTMLQDIKRQPKVVERLLSLPLEYWSQFMMVEQENIDPLHVIENSNAFSTPQTPDIKVSLLGP |
| AVPNPDPVTMLQDIK.QPKVVE.LLSL.LEYW.QF.M.EQENID.LHVIENSNAFSTPQTPDIKVSLLGP | |
| Retrocopy | AVPNPDPVTMLQDIKCQPKVVEHLLSLSLEYWNQFIMMEQENIDALHVIENSNAFSTPQTPDIKVSLLGP |
| Parental | VTTPEHQLLKTPSSSSLSQRVRSTLTKNTPRFGSKSKSATNLGRQGNFFASPMLK |
| VTTP..QLLKTPSS.SLS.R..STL.KNTPRFG.KSKSATNLG.QGNFFASPMLK | |
| Retrocopy | VTTPKCQLLKTPSSGSLS*RIHSTLNKNTPRFGRKSKSATNLG*QGNFFASPMLK |
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 | 19 .28 RPM |
| SRP051959_heart | 0 .02 RPM | 2 .32 RPM |
| SRP051959_kidney | 0 .00 RPM | 2 .53 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .49 RPM |
| SRP051959_lung | 0 .03 RPM | 8 .83 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 17 .05 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .59 RPM |
| SRP051959_spleen | 0 .02 RPM | 9 .94 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_837 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_837 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_837 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 ,
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