RetrogeneDB ID: | retro_mdom_1109 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:132091797..132093209(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CCNT2 | ||
| Ensembl ID: | ENSMODG00000000727 | ||
| Aliases: | None | ||
| Description: | cyclin T2 [Source:HGNC Symbol;Acc:1600] |
Retrocopy-Parental alignment summary:
>retro_mdom_1109
CTTACTGCCTTTTGCCTTCAATATAAACCAACAGTGACAGCATGTTTGTGCATTCACTTGTCCTGCAAGTGGTCCAATTG
GGAGATTCCTGTATCTACTGATTGAAAGCATTGGTGTGAATATGTGAATCCATCAGTTACCTTAGAATTACTAGATGAAT
TGACTCACAAGTTCCTACAAATTTTGTAGAAAACTCCTAATAGATTGAAGAGGATATGGAAATGAAGGGCTAATCAGGTG
GCTAGAAAATCAAAAGGGGATGGACAGGTGTCTAAAACAGCTCTTCTTGGTTCATCTCTGGCACAGAATTCCATTTTAGT
AGCTAGTGTTACTCATGTGACTGCAAATGCAAGCTTTCAAAAACCATCTATCTCAGCATTTCCTGCTCCAGTACCTCTGA
ATTCAGGAAATATTTCTGTTCAGGATAGTCATACATCTGATAATTTGGCAATACTAATGACAGGAATGCAAAGTACCTCA
TACAGTTTGGGATCACACCAAGAATGGCCTCAACATCAAGAACCAAGAAGGACAGAACAAATATATTCACAGAAACAGAA
GGGTTCAATGTCTGGAAGTCAATACAACATCAACTTCCAGCAAGGAGTTGCTGAGTCATTACATTCAGGATTACATCACA
GGTCTGACAAACTGATCATTCTTCAGTTAAACAAGAATATATTCACAAGGCAGGAAGCAGCAAACGCCATGGGCCAGTTT
CTTCTGCTTCTGTAATAGTTCCTCAGAAAATGTCATTAGATAAATAGAGAGGGAAATGAAAGCTAGAACCACTTGAACTG
GATGTAGGGGAACATTATGTAGCTGCCCAAACAGAGAAGCCCCACAAAAAACACATGAATTGCAGGCAGCCAACAGCAGT
TCTGTAACTTCTCTTATTAAAATGAAAATTCCTATTGCGAATGCAGAGAAACCAGAAAAAATACATTTTGGATAAAAAAG
TAAAAGAGTGGATCACTTAAACTGCGAACTCCAATTCCCCCCCCCCCCACTGATAAAAGTTCTAGTAAAGAAGAACTGAA
AATGAAAATAAATTTTCTTCTTTGGAAAGGCACAGTTCTTCTGATGGGGGCAGTGGAAAGAGCAAGCATTCAAGCCCACA
TGTGAGTAAAGACCACAAAGAAAAGTACAAGGAATATTCCTCCAACCACCATCACAGTAGCAGACACAAACATTCCCATT
CACATAGTGGCAGCAGTACTAGTGGCAATAAGCATAGTACTGATGGAATATCATCCACGGTTCTGAGGATTCCTGTTGGC
CTGAGTAGTGATGGTGGCAATTCCTCTAGTTCCAGTGCTACAAGAAAGAAGTTGCACATCAATGTTGCATCTCACAACTA
CCACTCCAAAATGAGTGAAAGTTCCAAAAGTTCAGGTGGACTACTGACATCT
ORF - retro_mdom_1109 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.5 % |
| Parental protein coverage: | 64.03 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | LTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPSVTLELLDELTHEFLQILEKTPNRLK |
| LT.FCLQYKPTV.AC.CIHL.CKWSNWEIPVSTD.KHW.EYV.PSVTLELLDELTH.FLQIL.KTPNRLK | |
| Retrocopy | LTAFCLQYKPTVTACLCIHLSCKWSNWEIPVSTD*KHWCEYVNPSVTLELLDELTHKFLQIL*KTPNRLK |
| Parental | RIRNWRATQAARKPKGDGQVSETALLGSSLVQNSILVDSVTGVTTNASFQKPSTSAFPAPVPLNSGNISV |
| RI...RA.Q.ARK.KGDGQVS.TALLGSSL.QNSILV.SVT.VT.NASFQKPS.SAFPAPVPLNSGNISV | |
| Retrocopy | RIWK*RANQVARKSKGDGQVSKTALLGSSLAQNSILVASVTHVTANASFQKPSISAFPAPVPLNSGNISV |
| Parental | QDTHASDNLTILTTGMPSTSYSLASHQEWPQHQEPTRTEQIYSQKQEAPMSGSQYNINFQQGPAGPLHSG |
| QD.H.SDNL.IL.TGM.STSYSL.SHQEWPQHQEP.RTEQIYSQKQ...MSGSQYNINFQQG.A..LHSG | |
| Retrocopy | QDSHTSDNLAILMTGMQSTSYSLGSHQEWPQHQEPRRTEQIYSQKQKGSMSGSQYNINFQQGVAESLHSG |
| Parental | LHHRSDKLSDHSSVKQEYTHK-AGSSKHHGPVSAAPVIVPQKMSLDKYREKRKLETLELDVREHYVAAQT |
| LHHRSDKL......K...T.....S..H.GPVS.A.VIVPQKMSLDK.R.K.KLE.LELDV.EHYVAAQT | |
| Retrocopy | LHHRSDKLIILQLNKNIFTRQ<GSSKRH-GPVSSASVIVPQKMSLDK*RGK*KLEPLELDVGEHYVAAQT |
| Parental | EQPHKKHM-QLQAASSSSVTSPIKMKIPIANAEKPE-KYMLDKKE-KSGSLKLRIPI--PPTDKSSSKEE |
| E.PHKKHM..LQAA.SSSVTS.IKMKIPIANAEKPE.KY.LDKK..KSGSLKLR.PI....TDKSSSKEE | |
| Retrocopy | EKPHKKHM<ELQAANSSSVTSLIKMKIPIANAEKPE>KYILDKKV>KSGSLKLRTPIXXXXTDKSSSKEE |
| Parental | LKMKI-KVSSSERHSSSDEGSGKSKHSSPHVSKDHKEKHKEHSSNRHHSSSHKHSHSHSGSSSSGSKHST |
| LKMKI.K.SS.ERHSSSD.GSGKSKHSSPHVSKDHKEK.KE.SSN.HHSS.HKHSHSHSGSS.SG.KHST | |
| Retrocopy | LKMKI<KFSSLERHSSSDGGSGKSKHSSPHVSKDHKEKYKEYSSNHHHSSRHKHSHSHSGSSTSGNKHST |
| Parental | DGIPPTVLRSPVGLSSDGGNSSSSSAARKKLHINDASHNHHSKMSKSSKSSGSSSSS |
| DGI..TVLR.PVGLSSDGGNSSSSSA.RKKLHIN.ASHN.HSKMS.SSKSSG....S | |
| Retrocopy | DGISSTVLRIPVGLSSDGGNSSSSSATRKKLHINVASHNYHSKMSESSKSSGGLLTS |
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 |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 0 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1109 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1109 was not experimentally validated.
Retrocopy orthology:
Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000000727 | 2 retrocopies |
retro_mdom_1109 , retro_mdom_864,
|