RetrogeneDB ID: | retro_mdom_1861 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 8:126403668..126406479(+) | ||
| Located in intron of: | ENSMODG00000016591 | ||
Retrocopy information | Ensembl ID: | ENSMODG00000016607 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SMC1B | ||
| Ensembl ID: | ENSMODG00000007253 | ||
| Aliases: | None | ||
| Description: | structural maintenance of chromosomes 1B [Source:HGNC Symbol;Acc:11112] |
Retrocopy-Parental alignment summary:
>retro_mdom_1861
CTTAACCAGAAGCGGCCCCAATACATTAAAGCCAAGGAAAATACTTCACACAAAATTAAGAAACTGGAAGCTGCCAAAAA
GTCTCTACAGAATGCCCAGAAACAGTATAAGAAGCGAAAAGGAGATATGGATGAACTTGAAAAAGAAATGGTATCAGTAG
AGAAGGCAAGACAAGAATTTGAAGATCGAATGGAGGAAGAGAGCCAGAGCCAGGGGCGGGACCTGACTCTGGAGGAAAAC
CAAGTAAAGAAGTACCACAGGCTGAAGGAGGAAGCCAGTAAAAGAGCAGCCACCTTGGCCCAGGAGCTAGAAAAATTCAA
TCGTGACCAGAAGGCTGACCAAGACCGACTGGACTTAGAGGAGCGAAAGAAAGTTGAGACTGAGGCCAAGATCAAACAGA
AACTGAGGGAAATTGAAGAGAATCAAAAGCGAATTGAGAAACTGGAAGAATACATCACCACCAGCAAGCAGTCTCTGGAG
GAACAGAAAAAACTAGAGGGAGAACTAACTGAGGAGGTTAAGCTGGCTAAACAGCGCATTGATGAAATCAACAAGGAGCT
GAATCAAGTGATGGAGCAACTTGGTGATGCCAGAATAGACCGACAGGAGAGCAGCAGACAGCAAAGAAAGGCAGAGATAA
TGGAGAGTATCAAACGCCTCTACCCTGGTTCTGTTTATGGCCGTCTCATTGATCTATGCCAGCCAACACAGAAGAAGTAC
CAGATTGCTGTAACTAAGGTGCTGGGCAAAAATATGGATGCCATCATTGTGGACTCTGAGAAAACTGGCCGGGACTGTAT
TCAATACATCAAGGAACAGCGTGGGGAGCCTGAGACCTTCTTACCACTTGACTACCTAGAGGTGAAACCAACAGATGAGA
AGCTTAGGGAACTGAAGGGGGCCAAGCTGGTAATTGATGTTATTCGCTATGAGCCACCACACATCAAGAAGGCTCTACAG
TATGCCTGTGGCAATGCTCTGGTATGTGACAATGTTGAAGATGCCCGCCGCATTGCTTTTGGTGGCCACCAGAGACATAA
GACAGTTGCACTAGATGGGACACTCTTCCAAAAGTCTGGTGTCATCTCTGGGGGAGCAAGTGACCTCAAAGCCAAGGCCC
GCCGATGGGATGAGAAAGCAGTTGACAAACTGAAGGAGAAGAAAGAGCGCCTCACGGAGGAGCTGAAGGAACAGATGAAA
GCTAAGAGGAAGGAGGCTGAGCTGAGGCAGGTACAGTCTCAGGCTCATGGCTTACAAATGAGGCTCAAGTACTCCCAGAG
TGACCTGGAACAGACAAAGACCCGGCACCTTGCACTTAACCTACAGGAAAAGTCCAAGCTAGAGAGTGAGCTAGCTAATT
TTGGACCCCGTATCAATGACATCAAAAGGATCATCCAGGGCCGGGAACGAGAGATGAAAGATTTGAAGGAAAAGATGAAC
CAGGTAGAAGATGAGGTATTTGAGGAGTTCTGCCGAGAAATTGGAGTTCGCAATATTCGTGAATTTGAGGAAGAGAAAGT
AAAGCGGCAAAATGAAATAGCCAAGAAACGGCTTGAGTTTGAGAACCAGAAGACTCGCCTGGGTATTCAGCTAGATTTTG
AGAAAAACCAGCTAAAAGAGGACCAGGATAAGGTTCATATGTGGGAGCAGACAGTAAAGAAGGATGAGAATGAAATTGAA
AAGCTCAAAAAGGAGGAGCAGAGACACATGAAAATAATCGATGAAACCATGGCCCAGCTACAGGACCTTAAGAACCAGCA
TCTGGCAAAGAAATCTGAAGTCAATGACAAAAACCATGAGATGGAGGAGATCCGAAAAAAGTTGGGTGGGGCCAACAAAG
AAATGACCCACTTACAAAAGGAGGTAACCGCTATTGAGACAAAGTTAGAGCAGAAGCGGAGTGACCGGCACAATCTGTTG
CAGGCCTGCAAGATGCAGGACATCAAGCTGCCCCTGGCCAAAGGCACCATGGATGACATTAGTCAAGAAGAGGGGAGCTC
CCAAGGGGAGGAGTCTGGGAGTGGCTCTCAACGAACCTCCAATATCTATGCCCGTGAGGCCTTGATTGAGATTGACTACA
GTGACCTCTGTGAGGACCTCAAAGATGCTCAGGCTGAAGAGGAGATTAAACAGGAGATGAACACATTGCAGCAAAAACTG
ACTGAACAGCAGAGTGTGCTGCAGCGCATTGCAGCACCTAACATGAAAGCCATGGAAAAACTGGAGAGTGTGCGGGACAA
GTTTCAGGAGACATCAGATGAGTTTGAGGCAGCTCGAAAGCGGGCCAAAAAAGCTAAGCATGCCTTTGAGCAGATTAAGA
AGGAACGCTTTGATCGCTTCAATGCCTGTTTTGAGTCTGTGGCTACCAACATTGATGAGATCTACAAAGCCCTGTCCCGA
AACAGCAGTGCTCAGGCCTTCTTGGGGCCTGAGAACCCAGAGGAACCCTACCTAGATGGGATCAATTACAACTGTGTAGC
CCCTGGCAAACGCTTCCGACCCATGGACAACCTGTCTGGTGGGGAAAAGACTGTAGCAGCTCTTGCTTTGCTTTTTGCCA
TCCATAGCTACAAACCAGCTCCTTTCTTTGTCCTAGACGAGATTGATGCTGCATTAGATAACACCAATATTGGCAAGGTT
GCCAACTATATAAAAGAACAGTCAACTTGCAACTTTCAAGCTATTGTCATTTCACTGAAGGAAGAATTTTATACGAAGGC
CGAGAGTCTGATTGGTGTCTATCCTGAGCAAGGGGACTGTGTTATCAGCAAGGTACTGACATTTGACCTTACCAAATACC
CAGATGCCAAC
ORF - retro_mdom_1861 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.2 % |
| Parental protein coverage: | 72.88 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LNQKRPQYIKAKENTSHHLKKLETAKKAIRVSEKQCTKQEDDIQALEKELWDLDRTWRNFEKQVEEERLR |
| LNQKRPQYIKAKENTSH..KKLE.AKK......KQ..K...D...LEKE..........FE...EEE... | |
| Retrocopy | LNQKRPQYIKAKENTSHKIKKLEAAKKSLQNAQKQYKKRKGDMDELEKEMVSVEKARQEFEDRMEEESQS |
| Parental | RGRDIELEASQLDQYKELKEQVIKKVATMTQQLEKLQWEQRADEERLAFGDRRRAEVQGNLKQVKEQVED |
| .GRD..LE..Q...Y..LKE...K..AT..Q.LEK....Q.AD..RL....R...E.....KQ.....E. | |
| Retrocopy | QGRDLTLEENQVKKYHRLKEEASKRAATLAQELEKFNRDQKADQDRLDLEERKKVETEAKIKQKLREIEE |
| Parental | HNKRIEKLEEYTSTCIDCLKEKTQQEEALSEELEQSRVRMAEVNSELSRIGGELQNAHIDHHEGKRQQKK |
| ..KRIEKLEEY..T....L.E....E..L.EE......R..E.N.EL......L..A.ID..E..RQQ.K | |
| Retrocopy | NQKRIEKLEEYITTSKQSLEEQKKLEGELTEEVKLAKQRIDEINKELNQVMEQLGDARIDRQESSRQQRK |
| Parental | AEVLEFLKRLYPESVYGRLLDLCHPIHKKYQLAVTKLFGRYMVAIVVVSEKVARDCIRFLKEERAEPETF |
| AE..E..KRLYP.SVYGRL.DLC.P..KKYQ.AVTK..G..M.AI.V.SEK..RDCI...KE.R.EPETF | |
| Retrocopy | AEIMESIKRLYPGSVYGRLIDLCQPTQKKYQIAVTKVLGKNMDAIIVDSEKTGRDCIQYIKEQRGEPETF |
| Parental | LALDYLDIKPINERLREMKGSKMVIDVVQTQLPQLKKVIQFVCGNGLVCETVEEARHMAFDGPERLKTVA |
| L.LDYL..KP..E.LRE.KG.K.VIDV.....P..KK..Q..CGN.LVC..VE.AR..AF.G..R.KTVA | |
| Retrocopy | LPLDYLEVKPTDEKLRELKGAKLVIDVIRYEPPHIKKALQYACGNALVCDNVEDARRIAFGGHQRHKTVA |
| Parental | LDGTLFLKSGVISGGSSDLKLKARCWDEKEINKLKERRDQLIRELKDLMKIRRKETDLKQIQALVQGTHT |
| LDGTLF.KSGVISGG.SDLK.KAR.WDEK...KLKE....L..ELK..MK..RKE..L.Q.Q....G... | |
| Retrocopy | LDGTLFQKSGVISGGASDLKAKARRWDEKAVDKLKEKKERLTEELKEQMKAKRKEAELRQVQSQAHGLQM |
| Parental | RLKYSQNELETIKKKHLARFNKEQSQLQSELLNIESQYVMLSDGIEKRIRQITDFQEKIDKVEDEIFHDF |
| RLKYSQ..LE..K..HLA....E.S.L.SEL.N...........I..R.R...D..EK...VEDE.F..F | |
| Retrocopy | RLKYSQSDLEQTKTRHLALNLQEKSKLESELANFGPRINDIKRIIQGREREMKDLKEKMNQVEDEVFEEF |
| Parental | CEEIGVENIREYENQQVKQQQEIDKKRLEFEKLKTRLNIQLEYSHNQLKKKTNKVTTLKEAIVKDTEDLE |
| C.EIGV.NIRE.E...VK.Q.EI.KKRLEFE..KTRL.IQL....NQLK....KV........KD....E | |
| Retrocopy | CREIGVRNIREFEEEKVKRQNEIAKKRLEFENQKTRLGIQLDFEKNQLKEDQDKVHMWEQTVKKDENEIE |
| Parental | SLKKVEENCLQVVDDLMTKRQQLKDVCVAQNVSIEKAQGQVEEARKKFLISNREVGKMQKEMAAVQTALE |
| .LKK.E.......D..M...Q.LK....A............EE.RKK....N.E....QKE..A..T.LE | |
| Retrocopy | KLKKEEQRHMKIIDETMAQLQDLKNQHLAKKSEVNDKNHEMEEIRKKLGGANKEMTHLQKEVTAIETKLE |
| Parental | QQRLEKHNILLSCKVQDIEVALVAGSLDETIQQSEGRGLGEQAESTQSTVAAMYEREGALQIDYSSLAED |
| Q.R...HN.L..CK.QDI...L..G..D..I.Q.EG...GE...S........Y.RE....IDYS.L.ED | |
| Retrocopy | QKRSDRHNLLQACKMQDIKLPLAKGTMDD-ISQEEGSSQGEESGSGSQRTSNIYAREALIEIDYSDLCED |
| Parental | LKDLQSDKEIKAQLGLLEQQLATHEDILLKTTAPNLRALQNLQNVRDKFQESIDAFEASRKEARVCRQEF |
| LKD.Q...EIK.....L.Q.L......L....APN..A...L..VRDKFQE..D.FEA.RK.A......F | |
| Retrocopy | LKDAQAEEEIKQEMNTLQQKLTEQQSVLQRIAAPNMKAMEKLESVRDKFQETSDEFEAARKRAKKAKHAF |
| Parental | EQVKKKRYDLFSQCFEHVSVSIDQIYKKLCRNNSAQAFLSPENPEEPYLEGISYNCVAPGKRFMPMDNLS |
| EQ.KK.R.D.F..CFE.V...ID.IYK.L.RN.SAQAFL.PENPEEPYL.GI.YNCVAPGKRF.PMDNLS | |
| Retrocopy | EQIKKERFDRFNACFESVATNIDEIYKALSRNSSAQAFLGPENPEEPYLDGINYNCVAPGKRFRPMDNLS |
| Parental | GGEKCVAALALLFAVHSFRPAPFFVLDEVDAALDNTNIGKVSSYIREQTREQFQMIIISLKEEFYSKADA |
| GGEK.VAALALLFA.HS..PAPFFVLDE.DAALDNTNIGKV..YI.EQ....FQ.I.ISLKEEFY.KA.. | |
| Retrocopy | GGEKTVAALALLFAIHSYKPAPFFVLDEIDAALDNTNIGKVANYIKEQSTCNFQAIVISLKEEFYTKAES |
| Parental | LVGIYPEQGDCMFSRVLTLDLSLYPDSD |
| L.G.YPEQGDC..S.VLT.DL..YPD.. | |
| Retrocopy | LIGVYPEQGDCVISKVLTFDLTKYPDAN |
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_1861 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1861 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 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000007253 | 1 retrocopy |
retro_mdom_1861 ,
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