RetrogeneDB ID: | retro_cjac_1871 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:170064642..170066181(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DNM2 | ||
| Ensembl ID: | ENSCJAG00000006319 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1871
GGCAACCGCGGGATCGAAGAGCTGATCCCGCTGGTCACCAAGCTGCAGGATGACTTCAGTGCCATCAGTCAGAGCTGCCA
CGTGGCCCTGCTGCAGATCGCCGTGGTGGGCGGCCAGAGCGCAGGCAAGAGCTCGGTGCTGGAGAACTTTGTGGGCCAGG
ACTTCCTTCCCGGTGGTTCAGGTATCGTCACCGGGCAGCCTCTCATTATGCAGCTCATCTTCTCAAAAACAGAATATGCC
GAGTTTTTGCACTGCAAGTCCGAAAAGCTTACAGACTCTGATGGAGTCCAGCAGGAGATTGAAGCAGACACTAACAGGGT
CAACCAACAAAGGCATCTCCCCAGCGCCCATCAACCTTTGGGTCTACTCACCACATGTGCTGAACTTGACCCTCATCAAA
CTCCCAGGTATTGCCAAGGTGCCTGTGGGCGACCAGCCTCCAGACATCGAGTACCAGAGCAAGGACATGATCCTGCAGTT
CCTCAGCCGGAAAAGCAGCCTCATCCTGGCCGTCACGCCTGCCAACATGGACCTGGCCAATTGAGATGCTCTCAACCTGG
TCAAGAAGGTCGATCCCCAAGGCCTGCGGACCATCAGTGTCATCACCAGGCTTGACCTGATGGATGAGGGCACTGACACC
AGGGACGTCTTAAAGAACAAGATGCTCTCATTGAGATGAGGCTACATTGGTGTGGCAAACCACAGCCAGAAGGATATTGA
CTGCAAGGAGGACATCTGAGCAGCGCTGCAGCTGAGAGGAGGTTCTTCCTCTCCCACCCAGCCTACTGGCACTGACCCCA
TGGGCACACTGCACCTGCAGAAGACGTTGAATCAGTAACTGACCCACCACATCTGGGAGTCGCTGCTGGCCCTGTGTAGC
AAGCTCCAGAGCCAGCTGCTGTCCCTGGAAAATGAAGGGGAGCAGTACAAGAACTTCTGGCCTGATGACCCCACCCGCAA
AACCAAAGCCCTGCTACAGGTGGTCCAGAAGTTTGGGTTGGATTTTGAGAAGAAGATCGAGGGCTCAGGAGATCAGGTGG
ACACGCTGGAGCTCTCCGAGGGCGCCCGAATCAATCGCATCTGCCACGAGCGGTTCCCGTTTGAGCTGGTGAAGATGGAG
TTTGACGAGGACTTAAGATGGGAGATCCGCTACTCCATTAAGAACATCCACGGAGTCAGGACGTGGTTCTTCACCCCCGA
CATGGCCTTTGAGTCTATTGTGAAAAAAGAGATTGTAAAACTCAAAGAATCAAGTTTGAAGTGTGTTGATCTTGTGGTCT
CAGAGCTGGCCATGGTCGTTAAAAAGTGTGCCCAGAAGTTCAGCTTCAATCCCGGTTGTGAGAGGAGATGGAGCAAATCG
TCATCACTTGCATCTGGGAATGGGAGGGGAGAACCAAGGACCAGATTCTTCTGCTGAGCGACATCGAACAGTCCTACATT
AACACAAACCATGAGGACTTCATTGGCTTTGCCAGTGCCCAGCAGAGGAGCACACAGCTGAACAGGAAGAGGGCCATCCC
CAGTCAGGGGAAGATGCTG
ORF - retro_cjac_1871 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.27 % |
| Parental protein coverage: | 59.54 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | GNRGMEELIPLVNKLQDAFSSIGQSCHLDLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLIL |
| GNRG.EELIPLV.KLQD.FS.I.QSCH..L.QIAVVGGQSAGKSSVLENFVG.DFLP.GSGIVT..PLI. | |
| Retrocopy | GNRGIEELIPLVTKLQDDFSAISQSCHVALLQIAVVGGQSAGKSSVLENFVGQDFLPGGSGIVTGQPLIM |
| Parental | QLIFSKTEYAEFLHCKSKKFTDFDEVRQEIEAETDR-VTGTNKGISPVPINLRVYSPHVLNLTLIDLPGI |
| QLIFSKTEYAEFLHCKS.K.TD.D.V.Q..E.E.D.....TNKGISP.PINL.VYSPHVLNLTLI.LPGI | |
| Retrocopy | QLIFSKTEYAEFLHCKSEKLTDSDGVQQ--EIEADT>TGSTNKGISPAPINLWVYSPHVLNLTLIKLPGI |
| Parental | TKVPVGDQPPDIEYQIKDMILQFISRESSLILAVTPANMDLANSDALKLAKEVDPQGLRTIGVITKLDLM |
| .KVPVGDQPPDIEYQ.KDMILQF.SR.SSLILAVTPANMDLAN.DAL.L.K.VDPQGLRTI.VIT.LDLM | |
| Retrocopy | AKVPVGDQPPDIEYQSKDMILQFLSRKSSLILAVTPANMDLAN*DALNLVKKVDPQGLRTISVITRLDLM |
| Parental | DEGTDARDVLENKLLPLRRGYIGVVNRSQKDIEGKKDIRAALAAERKFFLSHPAYRHMADRMGTPHLQKT |
| DEGTD.RDVL.NK.L.LR.GYIGV.N.SQKDI..K.DI.A..A.......S.P......D.MGT.HLQKT | |
| Retrocopy | DEGTDTRDVLKNKMLSLR*GYIGVANHSQKDIDCKEDI*A--ALQLRGGSSSPTQPTGTDPMGTLHLQKT |
| Parental | LNQQLTNHIRESLPALRSKLQSQLLSLEKEVEEYKNFRPDDPTRKTKALLQMVQQFGVDFEKRIEGSGDQ |
| LNQ.LT.HI.ESL.AL.SKLQSQLLSLE.E.E.YKNF.PDDPTRKTKALLQ.VQ.FG.DFEK.IEGSGDQ | |
| Retrocopy | LNQ*LTHHIWESLLALCSKLQSQLLSLENEGEQYKNFWPDDPTRKTKALLQVVQKFGLDFEKKIEGSGDQ |
| Parental | VDTLELSGGARINRIFHERFPFELVKMEFDEKDLRREISYAIKNIHGVRTGLFTPDMAFEAIVKKQIVKL |
| VDTLELS.GARINRI.HERFPFELVKMEFDE.DLR.EI.Y.IKNIHGVRT..FTPDMAFE.IVKK.IVKL | |
| Retrocopy | VDTLELSEGARINRICHERFPFELVKMEFDE-DLRWEIRYSIKNIHGVRTWFFTPDMAFESIVKKEIVKL |
| Parental | KEPSLKCVDLVVSELATVIKKCAEKLSSYP-RLREETERIVTTYIREREGRTKDQILLLIDIEQSYINTN |
| KE.SLKCVDLVVSELA.V.KKCA.K.S..P.RL.EE.E.IV.T.I.E.EGRTKDQILLL.DIEQSYINTN | |
| Retrocopy | KESSLKCVDLVVSELAMVVKKCAQKFSFNP<RL*EEMEQIVITCIWEWEGRTKDQILLLSDIEQSYINTN |
| Parental | HEDFIGFANAQQRSTQLNKKRAIPNQGEIL |
| HEDFIGFA.AQQRSTQLN.KRAIP.QG..L | |
| Retrocopy | HEDFIGFASAQQRSTQLNRKRAIPSQGKML |
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 .04 RPM | 71 .89 RPM |
| SRP051959_heart | 0 .02 RPM | 33 .91 RPM |
| SRP051959_kidney | 4 .77 RPM | 42 .77 RPM |
| SRP051959_liver | 0 .00 RPM | 28 .74 RPM |
| SRP051959_lung | 0 .02 RPM | 52 .04 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 46 .48 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 26 .55 RPM |
| SRP051959_spleen | 0 .02 RPM | 46 .62 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1871 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1871 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1871 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 | ENSCJAG00000006319 | 1 retrocopy |
retro_cjac_1871 ,
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