RetrogeneDB ID: | retro_cjac_4136 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:6868749..6870125(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NOLC1 | ||
| Ensembl ID: | ENSCJAG00000017832 | ||
| Aliases: | None | ||
| Description: | nucleolar and coiled-body phosphoprotein 1 [Source:HGNC Symbol;Acc:15608] |
Retrocopy-Parental alignment summary:
>retro_cjac_4136
GCCATCTCCAAGAAGACTGTACCTTAAAGGAAAGCTGTGACCAAGATTCCAGTGAAAGCAGCTGCCAGCCCTATCCGAAA
GAGTTCCAGCAGTGAGGACCCCTCCAGTGAGGAGTAAGAGGAGTAGGAAAAAAGAATCATGAAAAAAAAAAAAAAAAAAC
AGGTCTCTAAAGTTCAGTTTCCCCTGCATGCTCCCCCATCAAAGAAGTCCTTGGGAACCCAGCCTCCCAAGAAAGCTGTG
GAGAAGGAAAAGCCTTCCAAAAGCAGCGATGAATCTGTTTCAAGTTTGCAGGAAGAGGAGAAACTCTGGCTAATGCAATC
ATCTCTAAAGCAACCACTAAACAACTTCCAGCAAAGAAAGCAGCAGAGAGCTCTTCAGACAGCTCTGAGACTCCAACAGC
TCTGAGGATGATGAAGTTCCTTCCAAGCCAGCCAGTACCAGCAAGAATTCCTCAAATAAGCCAGCTGCCACTACCAAGTC
ACGTGCAGTGGAGCCAGCTGCAACCCTCAAGCAACCAGTAAGCAGTGGCCAGAAGCCTCTGATGAGGAAGGCTGACAGTG
GCTCCAGTGAGGAAGAGAGCAGTTCCAGTGAGGAGGAGAAGACAAAGACGACTGTGGCCACTCCTAAGCCCAAGGTGACT
GACAAAGTAGCTCCATATCTGCCTGCCAAGCAGGCTCCTGAGGGTGGTAAGGACAGCAACTTTGATTCATACAGCTCTAG
CAGTGAAGAGGAGAAAGAGAAGACAGCTAAACCCCCAGTTAAAAAGAAGTTGAGGAAGCCAGCAGGAGGCACAGTCCTTT
CCAAGCCAGCCTCCACAAAGAAAGGAAAGGCCGAGAGCAGCCGCAGTTCTTCCTCTGATAACTCCAGTGAGGAGGAGGAA
GAGAAACCCAAAGGCAAGGGCTCTCCAAAATCACAAGTCCCCAGGACCAATGGCACCTCTGCTCTGACTTCCCACAATGG
AAAAGCACCTAAGAATAGTGAAGAGGAGGAAGAAGAAAAGAAAAAGGCAGCAGTGGCAGTTTCCAAGCTGAGTTCAGGAA
AGAAATGGATGCAGAATGAGGCTGCCACGGAGGCATATACTCCGCAAACCAAGAAGATAAAACTTCAGACACCTAACACA
TTTCCAAAAAGGAAGAAAGGAGGAAAAAAGGTATGATCCCCATCCTGAAGGGTCAGGGAGGAAGAAATTGAGGTGGCAGA
CAACTCCTTTGATGCCAACAACTGAGGTGCAGCCGGACAGAGGGAAACCAGCCAATCAAGCTTTGAAGTTCACCAAAGTC
AAATCCTTCTGGCGTGAGAAAACCAAGAAGAAGTAGGGCAGCTACTGGGCAGGCTCGATCTCTGTCCAGGTCAATTCTTT
AAAGTTTGACAGCAAG
ORF - retro_cjac_4136 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.44 % |
| Parental protein coverage: | 65.59 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | SVGEETVPKKQVVAKAPVKAAATPTQKSSSSEDSSSEE-EEQQKKPMKN-KPGPYSSVP-PPSAPPPKKT |
| .....TVP....V.K.PVKAAA.P..KSSSSED.SSEE.EE..K..MK..K....S.V..P..APP.KK. | |
| Retrocopy | AISKKTVP*RKAVTKIPVKAAASPIRKSSSSEDPSSEE*EE*EKRIMKKKKKKQVSKVQFPLHAPPSKKS |
| Parental | LGTQPPKKAVEKQQPVESSEDSSDESDSSSEEEKK-SPAKAVVSKATTKPPPAKKAAES-SSDSS-DSDS |
| LGTQPPKKAVEK..P......SSDES.SS..EE.K...A.A..SKATTK..PAKKAAES.S..S..DS.S | |
| Retrocopy | LGTQPPKKAVEKEKPSK----SSDESVSSLQEEEK<TLANAIISKATTKQLPAKKAAESSSDSSE<DSNS |
| Parental | SEEDEDPSKPAGTTKNSSHKPAGTTKSPAAKPAAAPKQSLGGGQKPLMRKADSSSSEEESSSSEEEKTKK |
| SE.DE.PSKPA.T.KNSS.KPA.TTKS.A..PAA..KQ....GQKPLMRKADS.SSEEESSSSEEEKTK. | |
| Retrocopy | SEDDEVPSKPASTSKNSSNKPAATTKSRAVEPAATLKQPVSSGQKPLMRKADSGSSEEESSSSEEEKTKT |
| Parental | TVATTKPKATAKAAPPLPAKQAPQGSRDSSSDSDSSSSEEEEEEKTSKTAVKKKPQEVAGGAAPSKPASA |
| TVAT.KPK.T.K.AP.LPAKQAP.G..DS..DS.SSSS.EEE.EKT.K..VKKK....AGG...SKPAS. | |
| Retrocopy | TVATPKPKVTDKVAPYLPAKQAPEGGKDSNFDSYSSSS-EEEKEKTAKPPVKKKLRKPAGGTVLSKPAST |
| Parental | KKGKPESSSSSSSDDSSEEEEEKPKGKGKGTPRPQALKASSTSALTAQNGKAAKNS-EEEEEKKKAAVAV |
| KKGK.ESS.SSSSD.SSEEEEEKP..KGKG.P..Q......TSALT..NGKA.KNS.EEEEEKKKAAVAV | |
| Retrocopy | KKGKAESSRSSSSDNSSEEEEEKP--KGKGSPKSQVPRTNGTSALTSHNGKAPKNSEEEEEEKKKAAVAV |
| Parental | SKPGSLKKRKQNEAAKEAETPQAKKIKLQTPNTFPKRKKGEKRASSPFRRVREEEIEVDSRVADNSFDAK |
| SK..S.KK..QNEAA.EA.TPQ.KKIKLQTPNTFPKRKKG.K...SP..RVREEEIEV....ADNSFDA. | |
| Retrocopy | SKLSSGKKWMQNEAATEAYTPQTKKIKLQTPNTFPKRKKGGKKV*SPS*RVREEEIEV----ADNSFDAN |
| Parental | RGAAG-DWGERANQVLKFTKGKSFRHEKTKKKRGSYRGGSISVQVNSVKFDSE |
| ...A..D.G..ANQ.LKFTK.KSF..EKTKKK.GSY..GSISVQVNS.KFDS. | |
| Retrocopy | N*GAA>DRGKPANQALKFTKVKSFWREKTKKK*GSYWAGSISVQVNSLKFDSK |
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 | 25 .47 RPM |
| SRP051959_heart | 0 .39 RPM | 24 .78 RPM |
| SRP051959_kidney | 0 .00 RPM | 26 .91 RPM |
| SRP051959_liver | 0 .00 RPM | 32 .21 RPM |
| SRP051959_lung | 0 .00 RPM | 29 .56 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 33 .90 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 31 .36 RPM |
| SRP051959_spleen | 0 .00 RPM | 29 .92 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4136 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4136 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4136 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 7 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000010062 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000017832 | 2 retrocopies |
retro_cjac_4136 , retro_cjac_4187,
|
| Homo sapiens | ENSG00000166197 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000015012 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000002595 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000023882 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000014974 | 1 retrocopy |