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 symbol: XPO1
• Ensembl ID: ENSMODG00000002831
• Aliases: None
• Description: exportin 1 (CRM1 homolog, yeast) [Source:HGNC Symbol;Acc:12825]

Sequence

>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

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1971 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1971 was not experimentally validated.

Homology

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.

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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	retro_ogar_2982,