RetrogeneDB ID: | retro_cjac_1881 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:419979..421119(-) | ||
| Located in intron of: | ENSCJAG00000010221 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PAK2 | ||
| Ensembl ID: | ENSCJAG00000013687 | ||
| Aliases: | None | ||
| Description: | p21 protein (Cdc42/Rac)-activated kinase 2 [Source:HGNC Symbol;Acc:8591] |
Retrocopy-Parental alignment summary:
>retro_cjac_1881
GTGTCTGATAACGGAGAAATGGAAGACAAGCCTCCAGCACCTCCTGTGGGAATGAGCAGTACCATTTTTAGCACTGGAGG
CAAAGATCCTTTGTCAGCCAATCATAGTTTGAAACCTTTGCCCTCTGTTCCAGAGGAGAAAAAGCCCAGGAATAAAATCA
TCTCCATATTCTCAGGCAAAGAAACAGAAGTAAAAAGAAAGAAAAGGAATGGCCAGACATTTCTCCTCCATCTGATTTTG
AACACACTATCCATGTTGGCTTTGATGCTGTTACAGGAGAATTCACTGGCATGCCAGAACAGTGGGCTTGATTACTACAG
ACCTCCAATATCACCAAACTAGAGCAAAAGAAGAATCCTCAGGCTGTGCTGGATGTCTCAAAGTTCTACGGCTCCAACAC
AGTGAAGCAGCAAAAATATCTGAGCTTTACTCCTCCTGAGAAAAATGGCTTCCCTTCTGCAACACCACCACTGAATGCCA
AGGGACCAGAAACATCAGCAGTAGTGACAGAGGAAGATGATGATGATGATGAAGAAACCGCTCCTCCTGTTACTGCCCCA
GGACCAGATCATACAAAATCAATTTACACATGGTCTGTAATTGACCGTTTCTGCACCAGTTGGTGATTCAAACGTTGATG
GTGGTGCCAGGTCTTCAGACAAACAGAAAAAGAAGACTAAGATGACAGATGAAGAGATTATGGAGAAATTCAGAACTACT
TTGAGCATAGGTGACCCTAAGAAACAATACACAAGATATGCAAAAATTGGTCAAGGGACTTCTGGTACATTTTCACTGCT
ACTGATGCATTGGGAGAGGAGGTTGCATCAAACAGATTTACAGAAACAGCCAAAGAAGGAATTGATCATTAACGATATTC
TGGTGATGAAAGAATTAAAAAATCCCAACATATTTAACTTCTTGGACAATTACCTGGTAGGAGATTAATTGTTTGTGGTA
ATGGGAGTAACTTGCTGGTGGATCACTTACTGTCGTTGTATCAGAAACCTGTATGGATGAAGCACAGATTGCTGCTGTAT
GCAGAGAGTGTTTCAGGCACTGGGGTTTTTACATGCTAATCAAGTGATCCACAGAGACATCAAAAGTGACAATGTACTTT
TGGGAATGGAAGGATCAGTT
ORF - retro_cjac_1881 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.03 % |
| Parental protein coverage: | 72.9 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | MSDNGELEDKPPAPPVRMSSTIFSTGGKDPLSANHSLKPLPSVPEEKKPRNKIISIFSGTE-KGSKKKEK |
| .SDNGE.EDKPPAPPV.MSSTIFSTGGKDPLSANHSLKPLPSVPEEKKPRNKIISIFSG.E...SKKKEK | |
| Retrocopy | VSDNGEMEDKPPAPPVGMSSTIFSTGGKDPLSANHSLKPLPSVPEEKKPRNKIISIFSGKE<NRSKKKEK |
| Parental | ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWARLLQTSNITKLEQKKNPQAVLDVLKFYDSNTVKQ-K |
| E.P.ISPPSDFEHTIHVGFDAVTGEFTGMPEQWA.LLQTSNITKLEQKKNPQAVLDV.KFY.SNTVKQ.K | |
| Retrocopy | EWPDISPPSDFEHTIHVGFDAVTGEFTGMPEQWA*LLQTSNITKLEQKKNPQAVLDVSKFYGSNTVKQQK |
| Parental | YLSFTPPEKDGFPSGTPALNAKGSETSAVVTEEDDDDEETAPP-VIAPRPDHTKSIYTRSVIDPVPAPVG |
| YLSFTPPEK.GFPS.TP.LNAKG.ETSAVVTEEDDDD.E...P....P.........T......V.APVG | |
| Retrocopy | YLSFTPPEKNGFPSATPPLNAKGPETSAVVTEEDDDDDEETAP>LLLPQDQIIQNQFTHGL*LTVSAPVG |
| Parental | DSNVDGGAKSSDKQKKKTKMTDEEIMEKLRTIVSIGDPKKKYTRYEKIGQGASGT-VFTATDVALGQEVA |
| DSNVDGGA.SSDKQKKKTKMTDEEIMEK.RT..SIGDPKK.YTRY.KIGQG.SGT..FTATD.ALG.EVA | |
| Retrocopy | DSNVDGGARSSDKQKKKTKMTDEEIMEKFRTTLSIGDPKKQYTRYAKIGQGTSGT<IFTATD-ALGEEVA |
| Parental | -IKQINLQKQ-PKKELIINEILVMKELKNPNIVNFLDSYLVGDELFVVM-EYLAGGSLTDVVTETCMDEA |
| .IKQI....Q..K...I.N.ILVMKELKNPNI.NFLD.YLVGD.LFVVM.E.LAGGSLT.VV.ETCMDEA | |
| Retrocopy | <IKQIYRNSQ<KKELII-NDILVMKELKNPNIFNFLDNYLVGD*LFVVM>E*LAGGSLTVVVSETCMDEA |
| Parental | QIAAVCREC-LQALEFLHANQVIHRDIKSDNVLLGMEGSV |
| QIAAVCREC..QAL.FLHANQVIHRDIKSDNVLLGMEGSV | |
| Retrocopy | QIAAVCREC<FQALGFLHANQVIHRDIKSDNVLLGMEGSV |
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 .82 RPM | 40 .87 RPM |
| SRP051959_heart | 0 .54 RPM | 36 .12 RPM |
| SRP051959_kidney | 0 .42 RPM | 37 .65 RPM |
| SRP051959_liver | 0 .30 RPM | 34 .25 RPM |
| SRP051959_lung | 0 .81 RPM | 61 .46 RPM |
| SRP051959_lymph_node | 0 .98 RPM | 71 .28 RPM |
| SRP051959_skeletal_muscle | 0 .26 RPM | 28 .94 RPM |
| SRP051959_spleen | 0 .80 RPM | 60 .06 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1881 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1881 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1881 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000013687 | 1 retrocopy |
retro_cjac_1881 ,
|
| Homo sapiens | ENSG00000180370 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000013895 | 1 retrocopy |