RetrogeneDB ID: | retro_cjac_3922 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286253.1:65993..67710(+) | ||
| Located in intron of: | ENSCJAG00000012992 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ADAD1 | ||
| Ensembl ID: | ENSCJAG00000002796 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3922
AGCAACAACAATTGGTTTCAGAGTTTGCAGGCCCCCAGTTTTGCACAGATGCTGAAAAAGAACCTCCAGTTCAACCAGCC
ACACAGACGGTAACTACACCCACAGGATGTTTCTCAGAAAGTTATAGCCTGTCCAAGATAGCATCCAAAGTTACACAAGT
GACAGGTAATTTCCAGAACTGTTGCTTTCCAAGAGTCTTTCATCTATTTCAAATCCTGTCCTTCCTCCAAAAAAAAATAC
CTAAGGAATTTATAATGAAATACAAAGGTGGAGAGATAAATCCTGTGTCAGCCTTGCACCAGTTTGTACAAATGCAGTGA
GTTCAGCTTGACCTTAAGGAAACTGTGACAACAGATAATGTTATGGGACCGTATTTTGCCTTTTGTGCTGTGGTAGATGG
TATTCAGTACTAGACTGGACTGGGACAAAATAAAAAGGAGTCTAGATCCAATGCAGCAAAATTAGCTCTTGAGCTTCTGC
AATTGGATGAACCTGAACCACAAATTTTAGAAACATCAGATCCTCCTCCTTTCCCTGCAGAACCTACTGTTTTACCTGAA
CAGGCATATGTTTCAAAAGCACATTATGAAGGGAGATATATTCAGTATGCAAAGATTTCACAGATCGTTAAGGAAACATT
TAATCAACTAATTTCAAATCATTCAGAATGCCTGAAATGCAGCAATTCATTGGCTGCTTTTATAATTGAAAGAGCTGGAC
AGCATGAGGTTGTAGCTATAGGCACAGGTTAATACAACTACAGCCAGGGCATTAAACCAAATGGAAGAGTATTGCATGAT
ACTCATGCTGTCATTACAGCAAGAAGGTCTCTTCTTAGGTACTTTTACAGACCACTTCTACTCTTCTACAGCAAAAATCC
TGCTATGATGGAAAAATCAATATTCTGTACAGAACCAACTTCTAATCTACTCACTCTTAAACAGAATATCAACATTTGTC
TTTACATGAACCAGTTGCCTAAAGGATCAGCCCGGATTAAGTCACACTTACGTCTTAATCCACATTCTATATCTGCATTC
GAAGCCAATGAAGAACTGTGTCTCCATGTGGCTGTTGAAGGCAAAATTTATTGACTGTTTACTGTCCTAAAGATGGTGTT
AATAGAATAAGCAGTATGTCCTCAAGTGACAAATTGACAAGATGGGAAGTGTTTGGTATACAGGAAGCATTGCTGAGTCA
TTTTATACAGCTAGTTTACATCAGCAGTATACTGGTTGGTGATGGGAATTGCAATGATACCAGAGGCTTCAAAATCGCTA
TAAAGCAATGTGTTGATGATGCACTCACTTCAAAACTTCCTGTGTTTTACTTAGTCAACAGACCTCATATTAGTTTAGTG
CCCTCGGCATATCCACTTCAAATGAACTTGGAATATAAATTTCTGAGTCTGAATTGGGCACAAGGAGATGTTTCTTTGGA
GATTGTGGATGGCCTGAGTGGGAAGATCACTGAAAGTTCCCCATTTAAAAGTGGTATGTCAATGGCAAGTCAGCTTTGCA
AGGCTGCAATGTTAAGTCAATTTAACGTCCTTGCCAAAGAAGCTAAAAAAGAATTACCTGAAGCTGGTACATATCATGCA
GCTAAGTGTATGTCTTCCTCCTATCAATAAGCTAAATCTAAGCTGAAATCCTACTTACAACAACATGGCTATGGATCCTG
GATTGTGAAATCTCCCTGCATAGAGCAATTTAATATG
ORF - retro_cjac_3922 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.22 % |
| Parental protein coverage: | 99.83 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | ASNNWFQSSQVPSFAQMLKKNL-PVQPATQMVTTPTGCFSESYSLSKMASKVTPVTGNF-PEPMLSKSLS |
| ..NNWFQS.Q.PSFAQMLKKNL.PVQPATQ.VTTPTGCFSESYSLSK.ASKVT.VTGNF.PE..LSKSLS | |
| Retrocopy | SNNNWFQSLQAPSFAQMLKKNL<PVQPATQTVTTPTGCFSESYSLSKIASKVTQVTGNF<PELLLSKSLS |
| Parental | SISNPVLPPKK-IPKEFITKYKRGEINPVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQY |
| SISNPVLPPKK.IPKEFI.KYK.GEINPVSALHQF.QMQ.VQLDLKETVTT.NVMGPYFAFCAVVDGIQY | |
| Retrocopy | SISNPVLPPKK>IPKEFIMKYKGGEINPVSALHQFVQMQ*VQLDLKETVTTDNVMGPYFAFCAVVDGIQY |
| Parental | KTGLGQNKKESRSNAAKLALDELLQLDEPEPQVLETSALKEFPEHPVELSKK-YIGMVFFLLKKVQVLEI |
| .TGLGQNKKESRSNAAKLAL.ELLQLDEPEPQ.LETS....FP..P..L....Y...........Q...I | |
| Retrocopy | *TGLGQNKKESRSNAAKLAL-ELLQLDEPEPQILETSDPPPFPAEPTVLPEQAYVSKAHYEGRYIQYAKI |
| Parental | SNFFKKRSNTSRCRRNSHILYSTKLEMLLFLLAGQLEVVAIGTGEYNYSQSIKPNGRVLHDTHAVVTARR |
| S...K...N............S..L.......AGQ.EVVAIGTG.YNYSQ.IKPNGRVLHDTHAV.TARR | |
| Retrocopy | SQIVKETFNQLISNHSECLKCSNSLAAFIIERAGQHEVVAIGTG*YNYSQGIKPNGRVLHDTHAVITARR |
| Parental | SLLRYFYRQLLLFYSKNPAMMEKSIFCTEPTSNLLTLKQNINICLYMNQLPKGSAQIKSQLRLNPHSISA |
| SLLRYFYR.LLLFYSKNPAMMEKSIFCTEPTSNLLTLKQNINICLYMNQLPKGSA.IKS.LRLNPHSISA | |
| Retrocopy | SLLRYFYRPLLLFYSKNPAMMEKSIFCTEPTSNLLTLKQNINICLYMNQLPKGSARIKSHLRLNPHSISA |
| Parental | FEANEELCLHVAVEGKIY-LTVYCPKDGVNRISSMSSSDKLTRWEVLGVQGALLSHFIQPVYISSILVGD |
| FEANEELCLHVAVEGKIY.LTVYCPKDGVNRISSMSSSDKLTRWEV.G.Q.ALLSHFIQ.VYISSILVGD | |
| Retrocopy | FEANEELCLHVAVEGKIY<LTVYCPKDGVNRISSMSSSDKLTRWEVFGIQEALLSHFIQLVYISSILVGD |
| Parental | GNCSDTRGLEIAIKQRVDDALTSKLPMFYLVNRPHISLVPSAYPLQMNLGYKFLSLNWAQGDVSLEIVDG |
| GNC.DTRG..IAIKQ.VDDALTSKLP.FYLVNRPHISLVPSAYPLQMNL.YKFLSLNWAQGDVSLEIVDG | |
| Retrocopy | GNCNDTRGFKIAIKQCVDDALTSKLPVFYLVNRPHISLVPSAYPLQMNLEYKFLSLNWAQGDVSLEIVDG |
| Parental | LNGKITESSPFKSGMSMASRLCKAAMLSRFNLLAKEAKKELLEAGTYHAAKCMSSSYQEAKSKLKSYLQQ |
| L.GKITESSPFKSGMSMAS.LCKAAMLS.FN.LAKEAKKEL.EAGTYHAAKCMSSSYQ.AKSKLKSYLQQ | |
| Retrocopy | LSGKITESSPFKSGMSMASQLCKAAMLSQFNVLAKEAKKELPEAGTYHAAKCMSSSYQ*AKSKLKSYLQQ |
| Parental | HGYGSWIVKSPCIEQFNM |
| HGYGSWIVKSPCIEQFNM | |
| Retrocopy | HGYGSWIVKSPCIEQFNM |
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 | 0 .00 RPM |
| SRP051959_heart | 0 .26 RPM | 0 .00 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .23 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .00 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .02 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3922 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3922 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3922 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000002796 | 1 retrocopy |
retro_cjac_3922 ,
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