RetrogeneDB ID: | retro_cjac_2203 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:177173465..177175800(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HDAC6 | ||
| Ensembl ID: | ENSCJAG00000002395 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2203
AGCCTAGAATATATTGATCTGATGGAAACAACACAGTACATGAATGAGGGAGAACTGCACGTCCTAGCAGACACCTGTGA
CCCAGTTTATTTTCATCTGAACTCATACTCATGTGCCTGCCTGGCCTCAGCCTCTGTCCTCAGGCTGGTGGATGTGGTCC
TGGGGGCTGGAATCTGGAATGGCATGGCATCATTAGGCTTCCTGCACATCATGCCCAGCACAGTTTTATGGATGGCTGTT
GCATATTCAGTCACATGGTTGTGGCAGCCTGCTATGCTCAATAGAAACACCACATCCGGAGGGTCTTTGTGGTGGATTGG
GATGTGCACCACAGTCAAAAGCACAGTTCACCTTCAACCAGGACCCCTGTGTCCTCTATTTCTTCATCCACCACTATGAG
CAGGGTAGGTTCTGGCCCCACCTGAAGGCCTCTAACTGGTCCACCACAGGTTTTGGTCAAGGCCAAGGATATACCATCAA
TATTCCTTGGAACCAGGTGGGTATGAGAGATGCTGACTATATTGCTGCTTTCCTTCACGTCCTGCTGCTGGTCATCCTTG
AGTTCCAGCCTCAGCTGGTCCTGGTGGCTACTGGATTTGATACCCTGCAAGGGACCCCAAGGGTGAGATGGCTGCCACTC
CAGCAGGGTTCACCCAGCTAACCCACCTGCTCATGGGTCTGGCAGGAGGCAAGCTGACTCTGTTTTTGGAGGGTGGCTAC
AACCTCTGCACCCTGGCTGAAGGCATCAGTGCTTCACTCTACACCCTTCTGGGAGACCCTTGCCCTATACTGGAGTCCTC
TGGTGCCCGCTGCCAGAGTGCCCAGGCTTCAGTCTCCTGTGCTCTGGAAGCCCTTGAGCCCTTCTGAGAGGTTCTTGTGA
GATCAACTGAGACCAGGGAGGGGGACAACATGGAGGAGGACAATGTAGAAGAGAGAGAGGAGGAAGGACCTGGGAGCCCT
TGCTCCCAATCCTGACATGACCGGTGCTACAGTCTCACACAGGACTGGTCTCTGACAAAAGTATGATGAATCACTGCAAC
TTGTGGGACAGCCACCACCCCAAGGTACCCCAGGGCATCATGTGGATCATGTGCCGTCTGGAGGAGCTGGGGCTTGCTGG
GGGCTGCCTCACTCTGCCACGGCGCCCCTCCACAGACGCCGAGCTGTTCACCTGCCACAGTGCTGAGTACGTGGTGCATC
TCCAGGCCACAGAGAAGATGAAAACCCAGGAGCTGCACCGTGACAGCTTTGACTCTATCTACATCTGCCCCAGCACCTTC
GCCTGTGCACAGCTTGCCACTGGCACTGCCTGCTGCCTGGTGGAGGCCATGCTCTCAGGAGAAGTTCCGAATGGTGCTGC
AGTGGCATGTACCTCAGGACACCATGCGGAGCAGGACACAGCTTGTGGTTTTGCTTTTTAAACTCCGTGGCTGTGGCTGC
ATTCCATGCCCAGGCTATCAGTGGGTGTGTCCTGCGGATCCTGATCATGGATTGGGATGTTCACCATAGTAATGGAACTC
AGCACATGTTTGAGGATGACCCCAGTGTGCTATATGTGTCCCTGCACCGCTATGACACTGGCAACTTCTTCCCCATGGGA
GATGAGGGTGCCAGCAGCCAGATCAGCCAAGCTGCAGGCACAAGCTTCACCACCAATGTGGCATGGAATGGGCCCCTCAT
AGTTGATGCTGACTGCCTAGCTGCCTGGCATCACCTGGTGCTTCCCACTGCCTGCAAGTTTAACCCAGAACTGGTGTTGG
TTTCAGCTGGCTTTGACACTGCACGGGGGGACCTGCAGGGGAGCTTCCAGGTGTTATCTGAGGTTTACGCCCACCTCACC
TACCTGCTGATAGGTCTTGTCAGTGGCAGCATTATTCTTATCCTAGAGGGTGGCTATATGCTGACGTCCATCTCAGAGTC
CATGGCTGCCTGCACTTGCTCCCTCCTTGAAGACCAGCCAACCGTCCTGACCCTGCCAGGGCCCCCACTATCAGGGTCCC
TGGCCTCAATCACTGAGACCATCCAAGTCCATCATAGATACTGGCCCAGCTTACGGGTCATGAAGGTAAAAGATAAAGAG
GGATTCTCCAGTTCTGAGTTGGTCACCAAGAAGGCACCCCACCCAGCCAAACCTAGGTTAGCTGAGTGAATGACAACATG
AGAAAAGAAGGTTCTGGAAGCAGGCATGGGGAAGGTCATCTCAGCATCATCTGGGGAAGAGTCCACTCTGGGTCGGACTA
AGTCAGAGACAGCTGTAGTGGCACTCACTGAGGACCAGTCCTCAGAGGCAGCCACTGGGGGAGCCATGCTGGCCCAGACC
ATCTCCAAGGCAGCC
ORF - retro_cjac_2203 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.2 % |
| Parental protein coverage: | 63.73 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | SLEYIDLMETTQYMKEGELRVLADTYDSVYLHPNSYSCACLATGSVLRLVDAVLGAEIRNGMA-IIRPPG |
| SLEYIDLMETTQYM.EGEL.VLADT.D.VY.H.NSYSCACLA..SVLRLVD.VLGA.I.NGMA.IIR.P. | |
| Retrocopy | SLEYIDLMETTQYMNEGELHVLADTCDPVYFHLNSYSCACLASASVLRLVDVVLGAGIWNGMA<IIRLPA |
| Parental | HHAQHSLMDGYCMFNHVAVAARYAQQKHRIQRVLIVDWDVHHGQG-TQFTFDQDPSVLYFSIHRYEQGRF |
| HHAQHS.MDG.C.F.H..VAA.YAQ.KH.I.RV..VDWDVHH.Q...QFTF.QDP.VLYF.IH.YEQGRF | |
| Retrocopy | HHAQHSFMDGCCIFSHMVVAACYAQ*KHHIRRVFVVDWDVHHSQK<AQFTFNQDPCVLYFFIHHYEQGRF |
| Parental | WPHLKASNWSTIGFGQGQGYTINVPWNQVGMRDADYIAAFLHVLLPVTLEFQPQLVVVAAGFDALQG-DP |
| WPHLKASNWST.GFGQGQGYTIN.PWNQVGMRDADYIAAFLHVLL.V.LEFQPQLV.VA.GFD.LQG.DP | |
| Retrocopy | WPHLKASNWSTTGFGQGQGYTINIPWNQVGMRDADYIAAFLHVLLLVILEFQPQLVLVATGFDTLQG<DP |
| Parental | KGEMAATPAGFAQLTHLLMGLAGGKLILSLEGGYNLRALAEGVSASLHTLLGDPCPMLESPGAPCRSAQA |
| KGEMAATPAGF.QLTHLLMGLAGGKL.L.LEGGYNL..LAEG.SASL.TLLGDPCP.LES.GA.C.SAQA | |
| Retrocopy | KGEMAATPAGFTQLTHLLMGLAGGKLTLFLEGGYNLCTLAEGISASLYTLLGDPCPILESSGARCQSAQA |
| Parental | SVSCALEALEPFWEVLVRSTDTVEGDNVEEDNIEESEDERP-WEPPVLPILTWPVLQSRTGLVYDQSMMN |
| SVSCALEALEPF.EVLVRST.T.EGDN.EEDN.EE.E.E.P.WEP..LPILT.PVLQS.TGLV.D.SMMN | |
| Retrocopy | SVSCALEALEPF*EVLVRSTETREGDNMEEDNVEEREEEGP<WEP-LLPILT*PVLQSHTGLVSDKSMMN |
| Parental | HCNLWDSHHPEVPQRILRIMCRLEELGLAGRCLTLPPRPATEAELFTCHSAEYVARLRATEKMKTRELHR |
| HCNLWDSHHP.VPQ.I..IMCRLEELGLAG.CLTLP.RP.T.AELFTCHSAEYV..L.ATEKMKT.ELHR | |
| Retrocopy | HCNLWDSHHPKVPQGIMWIMCRLEELGLAGGCLTLPRRPSTDAELFTCHSAEYVVHLQATEKMKTQELHR |
| Parental | ESSNFDSIYICPSTFACAQLATGAACRLVEAVLSGEVLNGAAVVRPPGHHAEQDAACGF-CFFNSVAVAA |
| .S..FDSIYICPSTFACAQLATG.AC.LVEA.LSGEV.NGAAV....GHHAEQD.ACGF.CF.NSVAVAA | |
| Retrocopy | DS--FDSIYICPSTFACAQLATGTACCLVEAMLSGEVPNGAAVACTSGHHAEQDTACGF<CFLNSVAVAA |
| Parental | RHAQAISGHALRILIVDWDVHHGNGTQHMFEDDPSVLYVSLHRYDHGTFFPMGDEGASSQIGRAAGTGFT |
| .HAQAISG..LRILI.DWDVHH.NGTQHMFEDDPSVLYVSLHRYD.G.FFPMGDEGASSQI..AAGT.FT | |
| Retrocopy | FHAQAISGCVLRILIMDWDVHHSNGTQHMFEDDPSVLYVSLHRYDTGNFFPMGDEGASSQISQAAGTSFT |
| Parental | VNVAWNGPRIGDADYLAAWHRLVLPIAYEFNPELVLVSAGFDAARGDPLGGCQISPEGYAHLTHLLMGLA |
| .NVAWNGP.I.DAD.LAAWH.LVLP.A..FNPELVLVSAGFD.ARGD..G..Q...E.YAHLT.LL.GL. | |
| Retrocopy | TNVAWNGPLIVDADCLAAWHHLVLPTACKFNPELVLVSAGFDTARGDLQGSFQVLSEVYAHLTYLLIGLV |
| Parental | SGRIILILEGGYNLTSISESMAACTRSLLGDPPPLLTLPRPPLSGALASITETIQVHRRYWRSLRVMKVE |
| SG.IILILEGGY.LTSISESMAACT.SLL.D.P..LTLP.PPLSG.LASITETIQVH.RYW.SLRVMKV. | |
| Retrocopy | SGSIILILEGGYMLTSISESMAACTCSLLEDQPTVLTLPGPPLSGSLASITETIQVHHRYWPSLRVMKVK |
| Parental | DKEGPSSSKLITKKAPQPAKPMLAERMITREKKVLEASMGKVISV-SGEESTPDQVKSETAVVAVTQDQS |
| DKEG.SSS.L.TKKAP.PAKP.LAE.M.T.EKKVLEA.MGKVIS..SGEEST....KSETAVVA.T.DQS | |
| Retrocopy | DKEGFSSSELVTKKAPHPAKPRLAE*MTT*EKKVLEAGMGKVISASSGEESTLGRTKSETAVVALTEDQS |
| Parental | SKAATGGATLAQTVSKAA |
| S.AATGGA.LAQT.SKAA | |
| Retrocopy | SEAATGGAMLAQTISKAA |
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 | 11 .94 RPM |
| SRP051959_heart | 0 .00 RPM | 19 .87 RPM |
| SRP051959_kidney | 0 .00 RPM | 34 .19 RPM |
| SRP051959_liver | 0 .00 RPM | 25 .34 RPM |
| SRP051959_lung | 0 .02 RPM | 22 .01 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 19 .59 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 13 .30 RPM |
| SRP051959_spleen | 0 .00 RPM | 20 .46 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2203 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2203 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2203 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 | ENSCJAG00000002395 | 1 retrocopy |
retro_cjac_2203 ,
|