RetrogeneDB ID: | retro_cjac_544 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:71097533..71098737(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZNF362 | ||
| Ensembl ID: | ENSCJAG00000001133 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_544
AGGGTGGCCAAGCCTCGATTTAACAACCCCTACTTCTGGCCCCCTCCTCCCACCATGCCCAGCTAGCTGGATGACCTGGT
CCTGATTAACGAAATCAAGGAGCAGCTGATGGCCGAGAAGATCAGGCCACCTCACCTCAGCCTAGTCGCAGCAGCCGCTG
CTAGGGCCGCCGGCACACGCTGAGAGCAGCCAGGCCGTCATCTCGCTGCCCAAGCTGCAGCAGGTTCCGGGGCTGCATCC
GCAGGCAGTGCCGCAGCCCAACGTGGCGCTGCACGCACGGCCGGCCACCAGCACTGTCACAGGTCTGGGGCTGTCCACCC
AGACCCCGGCTGTGAGCACTTCTGAGTCGAGCACGGACACGGGCACGGGTACCAGCACCCCGTCCACACCCACCACCACC
AACCAGAGCCACCTCATCCCCTCGTCCCCCACCCTCATCTCAGGGATCACCAGCCCCCCTCTCCTGGACTCCATCAAGAC
AATCCAGGCCCATGGCCTGCTTGGCCCCTCCAAGTCCGAATGCAGCCTCAAAAAGATCAAGGCAGAGAACCCGGGGGATC
CGCCTGTCCTAGTAGTCCCCTACCCCATCCTGGCCTCGGGCAAGACTGCCAAGGAGGGCAAGATGTACAGGTGTAAGGTA
TGCCTGCTGACCTTTTTCACCAAGTCGGCTATGCAGATCCACTCCAAGTCGCACACAGAAGCCACGTACAAGTGCCTGTA
CTGCTCTTAAGTCCTTTGCCAATGCCTCCTACCTGGCCCAGCACCTGCGTATCCACCTGGGTGTCAAGCCCTACTACTGC
TCCTACTGTGATAAGTCCTTCCAGCAGCTCTCCCACCTCCAGCAGCACACCAGAATCCACACAGGCAACAGACCCTACAA
GTGCCCACATCCTGGCTGCGAGAAGGTTTTCACTCAGCTCTCCAACCTGCAGTCTCACCAGCGCTAGCACAACAAGGACA
AGCCCTACATGTGTCCCAGATGCTACGGGGCCTACTTGGACTCCGCCTCCCTGAAGATCCACCTCTCGGCCCACGCCATC
AAGCATGCCAAGGCCTACTGCTGCAGCATGTGTGGACAGGCCAAACCTCTGAGACCTACCTGATGATGAACATGTCCAAA
CACATGGTGGTGGAGCACCTGGTGAGCCATCACTCACCCCAGAGGACGAAGTCCCCCTGCATCCCGGTGCGAATCTCTCT
CATC
ORF - retro_cjac_544 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.55 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | RMAEPRFNNPYFWPPPPTMPSQLDNLVLINKIKEQLMAEKIRPPHLPP-TSASSQQPLLVPPAPAESSQA |
| R.A.PRFNNPYFWPPPPTMPS.LD.LVLIN.IKEQLMAEKIR....PP.TSA.SQQPLL.PPA.AESSQA | |
| Retrocopy | RVAKPRFNNPYFWPPPPTMPS*LDDLVLINEIKEQLMAEKIR----PP>TSA*SQQPLLGPPAHAESSQA |
| Parental | VMSLPKLQQVPGLHPQAVPQPDVALHARPATSTVTGLGLSTRTPAVSTSESSAGTGTGTSTPSTPTTTSQ |
| V.SLPKLQQVPGLHPQAVPQP.VALHARPATSTVTGLGLST.TPAVSTSESS..TGTGTSTPSTPTTT.Q | |
| Retrocopy | VISLPKLQQVPGLHPQAVPQPNVALHARPATSTVTGLGLSTQTPAVSTSESSTDTGTGTSTPSTPTTTNQ |
| Parental | SRLIASSPTLISGITSPPLLDSIKTIQGHGLLGPPKSERGRKKIKAENPGGPPVLVVPYPILASGETAKE |
| S.LI.SSPTLISGITSPPLLDSIKTIQ.HGLLGP.KSE...KKIKAENPG.PPVLVVPYPILASG.TAKE | |
| Retrocopy | SHLIPSSPTLISGITSPPLLDSIKTIQAHGLLGPSKSECSLKKIKAENPGDPPVLVVPYPILASGKTAKE |
| Parental | GKTYRCKVCPLTFFTKSEMQIHSKSHTEAKPHKCPHCS-KSFANASYLAQHLRIHLGVKPYHCSYCDKSF |
| GK.YRCKVC.LTFFTKS.MQIHSKSHTEA...KC..CS.KSFANASYLAQHLRIHLGVKPY.CSYCDKSF | |
| Retrocopy | GKMYRCKVCLLTFFTKSAMQIHSKSHTEA-TYKCLYCS>KSFANASYLAQHLRIHLGVKPYYCSYCDKSF |
| Parental | RQLSHLQQHTRIHTGDRPYKCPHPGCEKAFTQLSNLQSHQRQHNKDKPYKCPNCYRAYSDSASLQIHLSA |
| .QLSHLQQHTRIHTG.RPYKCPHPGCEK.FTQLSNLQSHQR.HNKDKPY.CP.CY.AY.DSASL.IHLSA | |
| Retrocopy | QQLSHLQQHTRIHTGNRPYKCPHPGCEKVFTQLSNLQSHQR*HNKDKPYMCPRCYGAYLDSASLKIHLSA |
| Parental | HAIKHAKAYCCSMCGRA-YTSETYLMKHMSKHTVVEHLVSHHSPQRTESPGIPVRISLI |
| HAIKHAKAYCCSMCG.A..TSETYLM..MSKH.VVEHLVSHHSPQRT.SP.IPVRISLI | |
| Retrocopy | HAIKHAKAYCCSMCGQA<QTSETYLMMNMSKHMVVEHLVSHHSPQRTKSPCIPVRISLI |
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 | 1 .55 RPM |
| SRP051959_heart | 0 .00 RPM | 8 .31 RPM |
| SRP051959_kidney | 0 .00 RPM | 6 .39 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .71 RPM |
| SRP051959_lung | 0 .00 RPM | 4 .75 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 3 .36 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .25 RPM |
| SRP051959_spleen | 0 .00 RPM | 3 .97 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_544 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_544 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_544 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000001133 | 2 retrocopies |
retro_cjac_1134, retro_cjac_544 ,
|