RetrogeneDB ID: | retro_cjac_3955 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286409.1:503148..504900(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PML | ||
| Ensembl ID: | ENSCJAG00000017890 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3955
ATGCAGCAGGAGCCTGCACCCGAACGACCTCCGGTGCCCCAGCAGGACCCCACCCGGCCCCACGCGCCCACCATGCCTCC
CCCCGACACCCCCTCTGAAGGCCGCCAGCCCAGCCCCAGCCACAGCCCTGCAGAACAAGCCACGGAGGAGTTCCAGTTTC
TGCGCTGCCAGAAATGCCAGGCCAAAGCCAAGTGCCCGAAGCTGCTGCCTTACCTGCACACGCTGTGCTCGGGATGCCTG
GAGGCGTCGGGCATGCAATGCCCTATCTGCCAGGCGCCCTGGACGCCAGGTGCAGACACACCTGCACTGGATAACGTCTT
TTTCGAGAGTCTGCAGCGGCGCCTGTCGGTGTACCGGCAGATCGTGGATGCACAGGCTGTGTGCACCCGCTGCAAAGAGT
CAGCCGACTTCTTGTGCTTTGAGTGCGAGCAGCTCCTCTGCGCCAAGTGCTTCGAGGCACACCAATGTTTCCTCAAGCAC
GAGGCCTGGCCCCTGGCAGAGCTGCGCAACCAGTCGGTGCGTGAGTTCCTGGACGGCACCCGCAAGACCAACAACATCTT
CTGCTCTAACCCCAACCACCGCACCCCTATGCTGACCAGCATCTACTGCCGCGACTGTTCCAAGCCGCTGTGCTGCTCGT
GCGTGCTCTTTGACAGCGGCCACACCGAGCTAAAGTGCGACATCAGCGCGGAGATCCAGCAGCGACCGGAGGAGCTGGAT
GCCATGACGCAGGCGCTGCAGGAGCAGGACTGCGCCTTCGGTGGGGCGCACGCGCAGATGCACGCGGCCGTCGGCCAGCT
GGGCCGCGTGCGGGCGGAAACCGAGGAGCTGATCCGCGCGGGCATGCGCCAGGTAGTAGCTCACGGGCAGGCGCAGGAGA
CCGAGCTGCTGGAGGCGGTGGAGGCGCGGTAGCAGCGCGACTACGAGGAGATGGCCAGCCGGCTGGGCCGCCTGGACGCT
GTGCTACAGCGCATCCGCACGGGCAGCGCGCTCGTGCAGAGGATGAAGTGCTATGCCTCGGACTAGGAGGTGCTGGAGAT
GCACGGTTTCCTGCGCCAGGCACTCTGCCGTCTGCGCTAGGAGGAGCCCCAGAGCCAGCAAGCTGCCTTGCGCACGGATG
GCTTCGACGAGTTCAAGGTGCGCCTGCAGGACCTCATCTCTTACATCACCCAGGGGACAGATGCAGCTGTATCCAAGAAA
GCCAGGCCAGAGGCTGCCAGCACTCCCAGGGACCCTATTGATGTTGACCTGCCCGAGGAGGCAGAGAGAGTGAAGGCCCA
GGACCAGGCCCTGGGGCTGGCTGAAGCCCAACCTGTGGCTGTGGTACAGTCATTCCCCGGGGCACACCTCGTGCCAGTGT
ACGCCTTCTCCATCAAAGGCCCTTCCTACAGAGAGGAGGTCTCCAATACAACCACAGGCCAGAAAAGGAAGATCATTCAG
ACCCAGCGCCTCAGGAAGGTCATCCAGGAGTCTGAGGAGGGTAAGGAGGCGAGGTTGGCTCGGAGCTCCCCCGAGCAGCC
CAGGCGTAGCACCTCTAAGGCAGTCTCACCACCCCACTTGGATGGGCCGCCCAGCGCCGGGACCCCCGACATGGGAAGTG
AGGCCATCCCACCCAACAGCAACCATGTGGCCAGTGGCGCCGGGGAGGCAGAGGAGTGCATTGTGGTGATCAGCAGCTCA
GAAGACTCAGATGCCGAAAACTCGTGCATGGAGCCCACGGAGACCGCCAAGCCACAGTCCTCGCCAGCCCAG
ORF - retro_cjac_3955 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.4 % |
| Parental protein coverage: | 66.4 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MQQEPAPARSPGPQQDTARPHAPTMPPPDTPSEGRQPSPSHSPAEQATEEFQFLRCQKCQAEAKCPKLLP |
| MQQEPAP.R.P.PQQD..RPHAPTMPPPDTPSEGRQPSPSHSPAEQATEEFQFLRCQKCQA.AKCPKLLP | |
| Retrocopy | MQQEPAPERPPVPQQDPTRPHAPTMPPPDTPSEGRQPSPSHSPAEQATEEFQFLRCQKCQAKAKCPKLLP |
| Parental | CLHTLCSGCLEASGMQCPICQAPWPPGADTPALDNVFFESLQRRLSVYRQIVDAQAVCTRCKESADFWCF |
| .LHTLCSGCLEASGMQCPICQAPW.PGADTPALDNVFFESLQRRLSVYRQIVDAQAVCTRCKESADF.CF | |
| Retrocopy | YLHTLCSGCLEASGMQCPICQAPWTPGADTPALDNVFFESLQRRLSVYRQIVDAQAVCTRCKESADFLCF |
| Parental | ECEQLLCAKCFEAHQWFLKHEARPLAELRNQSVREFLDGTRKTNNIFCSNPNHRTPTLTSIYCRGCSKPL |
| ECEQLLCAKCFEAHQ.FLKHEA.PLAELRNQSVREFLDGTRKTNNIFCSNPNHRTP.LTSIYCR.CSKPL | |
| Retrocopy | ECEQLLCAKCFEAHQCFLKHEAWPLAELRNQSVREFLDGTRKTNNIFCSNPNHRTPMLTSIYCRDCSKPL |
| Parental | CCSCALLDSGHSELKCDISAEIQQRQEELDAMTQALQEQDGAFGAAHAQMHAAVGQLGRARADTEELIRA |
| CCSC.L.DSGH.ELKCDISAEIQQR.EELDAMTQALQEQD.AFG.AHAQMHAAVGQLGR.RA.TEELIRA | |
| Retrocopy | CCSCVLFDSGHTELKCDISAEIQQRPEELDAMTQALQEQDCAFGGAHAQMHAAVGQLGRVRAETEELIRA |
| Parental | RVRQVVAHVQAQESELLEAVEARYQRDYEEMASRLGRLDAVLQRIRTGSALVQRMKCYASDQEVLDMHGF |
| ..RQVVAH.QAQE.ELLEAVEAR.QRDYEEMASRLGRLDAVLQRIRTGSALVQRMKCYASD.EVL.MHGF | |
| Retrocopy | GMRQVVAHGQAQETELLEAVEAR*QRDYEEMASRLGRLDAVLQRIRTGSALVQRMKCYASD*EVLEMHGF |
| Parental | LRQALCRLRQEEPQSLQAAVRTDGFDEFKVRLQDLISCITQGTDAAVSKQARPEAASTPRDPIDVDLPEE |
| LRQALCRLR.EEPQS.QAA.RTDGFDEFKVRLQDLIS.ITQGTDAAVSK.ARPEAASTPRDPIDVDLPEE | |
| Retrocopy | LRQALCRLR*EEPQSQQAALRTDGFDEFKVRLQDLISYITQGTDAAVSKKARPEAASTPRDPIDVDLPEE |
| Parental | AERVKAQAQALGLAEAQPVAVVQSVPGAHPVPVYAFSIKGPSYREEVSNTTTGQKRKSIQTQCPRKVIKM |
| AERVKAQ.QALGLAEAQPVAVVQS.PGAH.VPVYAFSIKGPSYREEVSNTTTGQKRK.IQTQ..RKVI.. | |
| Retrocopy | AERVKAQDQALGLAEAQPVAVVQSFPGAHLVPVYAFSIKGPSYREEVSNTTTGQKRKIIQTQRLRKVIQ- |
| Parental | ESEEGKEARLARSSPEQPRPSTSKAVSPPHLDGLPSAESPDIGSEVILPNSNHVASGAGEAEERIVVISS |
| ESEEGKEARLARSSPEQPR.STSKAVSPPHLDG.PSA..PD.GSE.I.PNSNHVASGAGEAEE.IVVISS | |
| Retrocopy | ESEEGKEARLARSSPEQPRRSTSKAVSPPHLDGPPSAGTPDMGSEAIPPNSNHVASGAGEAEECIVVISS |
| Parental | SEDSDAENSSSRELDDSSSESSDLQ |
| SEDSDAENS...........SS..Q | |
| Retrocopy | SEDSDAENSCMEPTETAKPQSSPAQ |
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 | 7 .41 RPM |
| SRP051959_heart | 0 .07 RPM | 4 .60 RPM |
| SRP051959_kidney | 0 .00 RPM | 6 .08 RPM |
| SRP051959_liver | 0 .02 RPM | 3 .77 RPM |
| SRP051959_lung | 0 .07 RPM | 8 .83 RPM |
| SRP051959_lymph_node | 0 .07 RPM | 8 .77 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .27 RPM |
| SRP051959_spleen | 0 .00 RPM | 11 .45 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3955 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3955 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3955 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 | ENSCJAG00000017890 | 1 retrocopy |
retro_cjac_3955 ,
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