RetrogeneDB ID: retro_mdom_773

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:424201852..424202959(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000016917
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OPTN
• Ensembl ID: ENSMODG00000016841
• Aliases: None
• Description: optineurin [Source:HGNC Symbol;Acc:17142]

Sequence

>retro_mdom_773
AAGAACAAATCTGTGGATGGGGCAAAGAATTATTTGGAATCTGAGGAATTAACTGTTAGCCAGCTTCTACTTTGTCTCAG
AGAAGGAAATCAGAAGGTGGAGAGACTTGAAACTGCACTCCAAGCAGCTAAAGACAAACTCTCAGATTTAGAAAAGAAGG
CAGAAGATCATTCCGAAAATGCTACCCAGACTGAGGAAGGCCCTGGAGAAGAAAAAGAAAAGGAGCAAAGCATAGAAACT
GTTGGAAGTGAAGTGGAAACACTGAACCTCCAAGTAACAGCTTTGTTTAAAGAGCTTCAAGAAGCTCACACTAAACTCAA
CGAAGCTGAGCTGATGAAGAAGAGACTCCAAGAAAAGTGTCAGGCCCTTGAAAGGAAAAATTCTGCAACCCCATCAGAGT
TGGATGAAAAGCAAGAATTAGTATATATCAACAAAAAGTTAGAGCTACAAGTGGAAAGTATGCGGTCAGAAATCAAAATG
GAACAAGCCAAAACAGATGATGAGAAGTCCAAATTTGCCATTTTACAGACTGCACACAACAAGCTTCTTCTTGAACATAG
TAATGCACTGAAAACAATTGAAGAACTAAAAAGGAAAGAGGCAGACAAAGTTGACAGATTAGTGATGACAGAACTAAATG
AAAAGCTTGAACTAGCAGAGAGAGCCCTGGCTTCCAAACAATTGCAAATGGATGAGATGAAGCAGACTATCGCTAAGCAA
GAAGAAGACCTGGAGACAATGTCGATCCTCCGAGCTCAGATGGAGGTTTATTGTTCTGACTTCCATGCTGAGAGGGCAGC
AAGAGAGAAGATTCATGAAGAAAAGGAGCAACTGGCATTACAGCTGGCATTTTTGTTGAAAGAAAATAATGTTTTTGAAG
ATGGAAGCAGACAGTCTTTGATGGAACTGCAAAGCCGTCATGGGGCCAGATCAACAAATGAACAAGACCAGCAGCCCTAC
CTTGTTCAGAGAGGAACTGATGATAGAAGCTGGCGGCAACAGCAACAGCAACAGCAAAGGAGCATTCCAATCCATTCCTG
CCCCAAGTGTGGAGAAATTCTGCCAGACATAGATACGCTGCAGATTCATGTTATGGATTGCATTATA

Alignment

ORF - retro_mdom_773 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.3 %
• Parental protein coverage: 57.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RNKSVDGAKNYLESEELTVSQLLLCLREGNQKVERLETALQAAKDKLSDLEKKAEDHSENATQTEEGPGE
          .NKSVDGAKNYLESEELTVSQLLLCLREGNQKVERLETALQAAKDKLSDLEKKAEDHSENATQTEEGPGE
Retrocopy KNKSVDGAKNYLESEELTVSQLLLCLREGNQKVERLETALQAAKDKLSDLEKKAEDHSENATQTEEGPGE

Parental  EKEKEQSIETVGSEVETLNLQVTALFKELQEAHTKLNEAELMKKRLQEKCQALERKNSATPSELDEKQEL
          EKEKEQSIETVGSEVETLNLQVTALFKELQEAHTKLNEAELMKKRLQEKCQALERKNSATPSELDEKQEL
Retrocopy EKEKEQSIETVGSEVETLNLQVTALFKELQEAHTKLNEAELMKKRLQEKCQALERKNSATPSELDEKQEL

Parental  VYINKKLELQVESMRSEIKMEQAKTDDEKSKFAILQTAHNKLLLEHSNALKTIEELKRKEADKVDRLVMT
          VYINKKLELQVESMRSEIKMEQAKTDDEKSKFAILQTAHNKLLLEHSNALKTIEELKRKEADKVDRLVMT
Retrocopy VYINKKLELQVESMRSEIKMEQAKTDDEKSKFAILQTAHNKLLLEHSNALKTIEELKRKEADKVDRLVMT

Parental  ELNEKLELAERALASKQLQMDEMKQTIAKQEEDLETMSILRAQMEVYCSDFHAERAAREKIHEEKEQLAL
          ELNEKLELAERALASKQLQMDEMKQTIAKQEEDLETMSILRAQMEVYCSDFHAERAAREKIHEEKEQLAL
Retrocopy ELNEKLELAERALASKQLQMDEMKQTIAKQEEDLETMSILRAQMEVYCSDFHAERAAREKIHEEKEQLAL

Parental  QLAFLLKENNVFEDGSSRQSLMELQSRHGARSTNEQDQQPYLVQRGTDDRSWRQQQQQQQRSIPIHSCPK
          QLAFLLKENNVFEDGS.RQSLMELQSRHGARSTNEQDQQPYLVQRGTDDRSW........RSIPIHSCPK
Retrocopy QLAFLLKENNVFEDGS-RQSLMELQSRHGARSTNEQDQQPYLVQRGTDDRSWXXXXXXXXRSIPIHSCPK

Parental  CGEILPDIDTLQIHVMDCII
          CGEILPDIDTLQIHVMDCII
Retrocopy CGEILPDIDTLQIHVMDCII

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	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

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_773 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_773 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000016841	1 retrocopy	retro_mdom_773 ,