RetrogeneDB ID: | retro_mdom_1971 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | Un:11065639..11068258(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000013587 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | XPO1 | ||
| Ensembl ID: | ENSMODG00000002831 | ||
| Aliases: | None | ||
| Description: | exportin 1 (CRM1 homolog, yeast) [Source:HGNC Symbol;Acc:12825] |
Retrocopy-Parental alignment summary:
>retro_mdom_1971
TGTGCAACGAATTCTCACATATTTCAGCTGTGTCAGTTTGTGATGGAAAATTCCCAAAATGCTTCACTTGTACATGCCAC
TTTGGAAACATTGCTAAGATTTCTTAACTGGATTCCACTGGGATATATATTCGAAACGAAGTTAATCAGCACATTAATAT
ATAAGTTTCTAAATGTTCCAATGTTTCGAAATGTCTCTCTGAAGTGCCTCACTGAGATTGCTGGTGTGAGTGTAAGCCAA
TATGAGGAACAATTTGTAACATTATTTGCACTGACAATGATGCAGCTTAAACAGATGATACCTTTAAACACCAATATTCG
ACTTGCTTACTCCAATGGAAAAGATGATGAACAAAATTTCATCCAGAATCTCAGTTTGTTTCTCTGTACCTTTCTTAAAG
AACATGGTCAACTTATCGAAAAGCGATTAAATCTCAGGGAAACATTGATGGAGGCTCTTCACTATATGTTGTTAGTATCT
GAAGTAGAAGAAACTGAAATCTTTAAGATTTGTCTTGAATATTGGAACCATCTAGCTGCTGAACTCTACAGAGAAAGTCC
ATTTTCAACATCTGCCTCTCCAATGCTCTCTGGAAGTCAACATTTTGATGTTCCTCCCAGGAGACAACTTTATCTACCTG
TATTATCCAAGGTCCGTTTATTGGTGGTGAGTCGAATGGCTAAGCCTGAAGAAGTTCTGGTTGTAGAAAATGATCAGGGA
GAAGTTGTTCGAGAATTTATGAAGGACACAGACTCCATTAATTTGTATAAGAATATGAGGGAAACATTAGTATACCTTAC
ACATCTGGATTATGCAGACACTGAAAGAATAATGACTGAAAAACTTCACAATCAGGTGAATGGAACAGAATGGTCTTGGA
AAAATTTGAACACTTTATGTTGGGCAGTAGGCTCTATTAGTGGAGCGATGCATGAAGAGGATGAAAAAAGGTTTCTTGTT
ACAGTCATAAAGGATCTTTTAGGATTATGTGAACAGAAAAGAGGCAAAGATAATAAAGCTATTATTGCATCAAATATCAT
GTACATAGTAGGTCAATATCCAAGGTTTTTGAGAGCTCATTGGAAATTTTTGAAGACCGTGGTCAACAAGTTATTTGAAT
TCATGCATGAAACTCATGATGGTGTCCAGGACATGGCCTGTGATACCTTCATAAAAATAGCACAAAAATGCCGCAGGCAT
TTTGTTCAGGTTCAGGTTGGAGAAGTAATGCCATTCATTGATGAAATTTTGAACAACATTAACACAATCATTTGTGATCT
TCAGCCTCAGCAGGTTCACACGTTTTATGAAGCTGTTGGATACATGATTGGTGCACAAACTGATCAAACAGTACAAGAAC
ATTTGATAGAAAAATATATGCTACTTCCTAATCAGGTGTGGGACAGCATAATTCAGCAAGCCACTAAAAATGTGGATATA
CTTAAGGATCCTGAAACAGTTAAGCAGCTTGGAAGTATTTTAAAAACAAATGTAAGAGCATGTAAAGCTGTTGGCCACCC
CTTTGTAATTCAACTTGGACGAATTTATTTAGATATGCTTAATGTGTACAAGTGCCTCAGTGAAAATATTTCTGCAGCTA
TCCAGGCCAATGGTGAAATGGTTACAAAACAACCCTTGATTAGAAGTATGCGAACAGTAAAAAGGGAGACTTTAAAATTA
ATATCTGGTTGGGTGAGCCGGTCTAATGATCCACAGATGATAGCAGAAAATTTTGTTCCTCCTTTGTTAGATGCAGTTCT
TATTGATTACCAGAGAAATGTTCCAGCTGCTAGAGAACCAGAAGTACTTAGTACTATGGCTATCATTGTCAACAAATTAG
GGGGACACATAACAACTGAAATACCTCAGATATTTGATGCTGTTTTTGAATGCACATTAAATATGATAAACAAGGACTTT
GAAGAATATCCTGAACACAGAACAAACTTTTTCTTACTACTTCAGGCCGTAAATTCTCATTGTTTCCCAGCATTCCTGGC
TATTCCACCTGCACAGTTTAAGTTAGTTTTGGATTCCATTATCTGGGCTTTCAAGCATACTATGAGGAATGTTGCAGATA
CAGGCCTACAGATACTTTTTACACTCTTGCAAAATGTTGCACAAGAAGAAACTGCTGCTCAGAGTTTCTATCAGACCTAT
TTCTGTGATATCCTTCAGCATATCTTTTCAGTTGTAACAGACACCTCACATACTGCTGGCTTAACGATGCATGCTTCAAT
TCTTGCCTACATGTTTAATTTAGTAGAAGAAGGAAAAATAAGTACACCATTAAATCCCGGAAATCCAGTTAACAACCAAA
TGTTTATTCAGGAGTATGTGGCTAATCTTCTCAAATCTGCTTTCCCTCACTTGCAGGATGCGCAAGTTAAACTGTTTGTA
ATAGGACTATTCAGTTTAAATCAAGATATCCCCGCCTTCAAAGAACACCTTAGAGATTTCCTGGTACAGATAAAGGAATT
TGCAGGTGAAGATACATCTGACCTGTTTTTAGAAGAAAGAGAAACAGCCCTTCCACAGGCTCAGGAAGAGAAACATAAAC
TTCAGATGTCTGTCCCTGGCATCCTTAATCCACATGAAATTCCTGAAGAAATGTGCGAT
ORF - retro_mdom_1971 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.59 % |
| Parental protein coverage: | 81.51 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | CNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGYIFETKLISTLIYKFLNVPMFRNVSLKCL |
| C...S.IFQLCQFVMENSQNA.LVHATLETLLRFLNWIPLGYIFETKLISTLIYKFLNVPMFRNVSLKCL | |
| Retrocopy | CATNSHIFQLCQFVMENSQNASLVHATLETLLRFLNWIPLGYIFETKLISTLIYKFLNVPMFRNVSLKCL |
| Parental | TEIAGVSVSQYEEQFVTLFTLTMMQLKQMLPLNTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHGQLIE |
| TEIAGVSVSQYEEQFVTLF.LTMMQLKQM.PLNTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHGQLIE | |
| Retrocopy | TEIAGVSVSQYEEQFVTLFALTMMQLKQMIPLNTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHGQLIE |
| Parental | KRLNLRETLMEALHYMLLVSEVEETEIFKICLEYWNHLAAELYRESPFSTSASPMLSGSQHFDVPPRRQL |
| KRLNLRETLMEALHYMLLVSEVEETEIFKICLEYWNHLAAELYRESPFSTSASPMLSGSQHFDVPPRRQL | |
| Retrocopy | KRLNLRETLMEALHYMLLVSEVEETEIFKICLEYWNHLAAELYRESPFSTSASPMLSGSQHFDVPPRRQL |
| Parental | YLPVLSKVRLLMVSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYADTERIMTE |
| YLPVLSKVRLL.VSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYADTERIMTE | |
| Retrocopy | YLPVLSKVRLLVVSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYADTERIMTE |
| Parental | KLHNQVNGTEWSWKNLNTLCWAIGSISGAMHEEDEKRFLVTVIKDLLGLCEQKRGKDNKAIIASNIMYIV |
| KLHNQVNGTEWSWKNLNTLCWA.GSISGAMHEEDEKRFLVTVIKDLLGLCEQKRGKDNKAIIASNIMYIV | |
| Retrocopy | KLHNQVNGTEWSWKNLNTLCWAVGSISGAMHEEDEKRFLVTVIKDLLGLCEQKRGKDNKAIIASNIMYIV |
| Parental | GQYPRFLRAHWKFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRRHFVQVQVGEVMPFIDEILNNI |
| GQYPRFLRAHWKFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRRHFVQVQVGEVMPFIDEILNNI | |
| Retrocopy | GQYPRFLRAHWKFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRRHFVQVQVGEVMPFIDEILNNI |
| Parental | NTIICDLQPQQVHTFYEAVGYMIGAQTDQTVQEHLIEKYMLLPNQVWDSIIQQATKNVDILKDPETVKQL |
| NTIICDLQPQQVHTFYEAVGYMIGAQTDQTVQEHLIEKYMLLPNQVWDSIIQQATKNVDILKDPETVKQL | |
| Retrocopy | NTIICDLQPQQVHTFYEAVGYMIGAQTDQTVQEHLIEKYMLLPNQVWDSIIQQATKNVDILKDPETVKQL |
| Parental | GSILKTNVRACKAVGHPFVIQLGRIYLDMLNVYKCLSENISAAIQANGKRLIFRKLGQSMRTVKRETLKL |
| GSILKTNVRACKAVGHPFVIQLGRIYLDMLNVYKCLSENISAAIQANG.......L..SMRTVKRETLKL | |
| Retrocopy | GSILKTNVRACKAVGHPFVIQLGRIYLDMLNVYKCLSENISAAIQANGEMVTKQPLIRSMRTVKRETLKL |
| Parental | ISGWVSRSNDPQMVAENFVPPLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITTEIPQIFDAVFE |
| ISGWVSRSNDPQM.AENFVPPLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITTEIPQIFDAVFE | |
| Retrocopy | ISGWVSRSNDPQMIAENFVPPLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITTEIPQIFDAVFE |
| Parental | CTLNMINKDFEEYPEHRTNFFLLLQAVNSHCFPAFLAIPPAQFKLVLDSIIWAFKHTMRNVADTGLQILF |
| CTLNMINKDFEEYPEHRTNFFLLLQAVNSHCFPAFLAIPPAQFKLVLDSIIWAFKHTMRNVADTGLQILF | |
| Retrocopy | CTLNMINKDFEEYPEHRTNFFLLLQAVNSHCFPAFLAIPPAQFKLVLDSIIWAFKHTMRNVADTGLQILF |
| Parental | TLLQNVAQEETAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKISTPLNPGNPV |
| TLLQNVAQEETAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKISTPLNPGNPV | |
| Retrocopy | TLLQNVAQEETAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKISTPLNPGNPV |
| Parental | NNQMFIQEYVANLLKSAFPHLQDAQVKLFVTGLFSLNQDIPAFKEHLRDFLVQIKEFAGEDTSDLFLEER |
| NNQMFIQEYVANLLKSAFPHLQDAQVKLFV.GLFSLNQDIPAFKEHLRDFLVQIKEFAGEDTSDLFLEER | |
| Retrocopy | NNQMFIQEYVANLLKSAFPHLQDAQVKLFVIGLFSLNQDIPAFKEHLRDFLVQIKEFAGEDTSDLFLEER |
| Parental | ETALRQAQEEKHKLQMSVPGILNPHEIPEEMCD |
| ETAL.QAQEEKHKLQMSVPGILNPHEIPEEMCD | |
| Retrocopy | ETALPQAQEEKHKLQMSVPGILNPHEIPEEMCD |
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 | 172 .48 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 | 153 .41 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1971 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1971 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000002831 | 1 retrocopy |
retro_mdom_1971 ,
|
| Otolemur garnettii | ENSOGAG00000000143 | 1 retrocopy |