RetrogeneDB ID: retro_mdom_777

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:440329214..440330900(+)
• Located in intron of: ENSMODG00000007674

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: OGFOD1
• Ensembl ID: ENSMODG00000013378
• Aliases: None
• Description: 2-oxoglutarate and iron-dependent oxygenase domain containing 1 [Source:HGNC Symbol;Acc:25585]

Sequence

>retro_mdom_777
GCATTTGCCACATGGCGCGTGACTTATAGTAGTCCCTGTGTCTCAGAGGTGAGGGGATCCAAAGGTATGAGTGGGAAACA
GCGCACGGATCAGGGACCTGTCTCAGAATGAAAGAAGAAGGGGAAGCACGAATTGACAGGAGAGTTCTCGGCTACTCTCT
GTGAGGAAACGGTGAAAACGCAGGTGGCTGAGGCCTGGAGCCGGAGGACCAGGTTCAGTCATGAGGCCATAATTATGGAC
CCAGATCCTTTCCAATACTGTGTGATCCCAAACTTCATCCAGTGCCAGACTTTCTTGGAGGGACTTCAGAAGGAACTTTT
GGATCTGGATTTCCATGAGAAATGCAATGACTTGTACAAATTCAAACAACTGGATGATCTGAAGAATAGAGACGAACTTC
ATATCTCTGTTTAAAGGAAAGTTCTGTTTGAATATTTTTGGAGATGACTTTCAGACATTGTTTTGATTGACTTGGAATCT
ACTGTTGATATCTCCTATGCTAAGTATTAGTATACAGATATCCCGTTATTCCATGATGATGAATTGGAAGGAAGAAGAAT
TGCTTTTATTCTATATCTTGTTCTTCCTTGGGACAAGAGCCTTGGTGGTACCTTGGACTTGTACAGTACAGATGAACATT
TCCAGTCGGAACAGACTGTTAAGTCTCTTGTCCCATCTTGGAACACCTTGGTTTTCTTTGAAGTGTCTCAAGTGTCCTAA
CATCAGGTTTCATAAGTTCTGTTTGAAGGAAAATGTCAGCTATCTATAAGTGGCTGGTTTCGTGGTCCTTCTCAGACAAG
GTCCTCAAGCTATTTTGAGCCCCTCCTACCTTGTAGCCCTCACATTTTACGAGATAATGAAATTTTATATGAATGGATTA
ACCCAATCTATATGGACATTGATTCCCAGGCTCAAATTCAAGAGGATTTTGAAGAGTGCTCTGAAATTCTGTTGAAGGAA
TTTTTCAAGTATGAAAAATATGAAAAAATATGTGAGGCTTTGGAGAAAGAAGATCTAGAATGGAGCAAACGAGGTCCCCC
CAATAAAAGGTTTTATGAAACAGCTAAGGAAGAGAAGCTTCCAGATATCTTAAGGGAATGCATGGAGTTATTTTGCTCTG
AGGTCCTGTTCTTGCTGCTGTCCAACTTCACAGGCCTGAAGCTTCATTTCCTGGTCTCTTCAGATGAGGATGATGAGGAC
CAGACAGACAATGATGAAGAAGAAAGTGAAGAAATTAGCCATGGTCCTTCTAAACAAGAAAACTACCAGGAGGCCAGTGG
CCACACAAGCCAACAAAGCAAGATAGAAACAGCTCTAGAATCAGAGAATGAAGAGGCAAAGAATAAATCAGCTGTCCCCA
CATGCACTGGAGAGCTGAGATATTGGAAGAATGTTCACTACACTTTAGTGCATGACACTAAAAATACTGAATTTGCCTTG
GACCTGCTTTTCTACTGTGGCTGTAAAGGATGGAAAACAGAATATGGTGGCTTTACTTCCTACACTGCCAAAGGTGAAGA
TGAAGAGCTCCTAATAGTGACTCCAGAAGAGAATTCACTGGCATTGGTTTACAGAGATTGAGAAACTCTAAAATTCATCA
AGCATATCAACCACCAACACTTAGAGCAAAAGAAAACTGGCCAGAACAGAACAGGTTTTTGGGACTTTTCCTTTGTCTAC
TATGAA

Alignment

ORF - retro_mdom_777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.86 %
• Parental protein coverage: 91.83 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AFAAWRATYSGHCVSEARGSKGMSGKRRADQGPVSERKKKGKRELTGEFSATLREETVKKQVAEAWSRRT
          AFA.WR.TYS..CVSE.RGSKGMSGK.R.DQGPVSE.KKKGK.ELTGEFSATL.EETVK.QVAEAWSRRT
Retrocopy AFATWRVTYSSPCVSEVRGSKGMSGKQRTDQGPVSE*KKKGKHELTGEFSATLCEETVKTQVAEAWSRRT

Parental  RFSHEAIIMDPDPFQHCVIPNFIQCQTFLEGLQKELLDLDFHEKCNDLYKFKQSDDLKNRDELHISALRK
          RFSHEAIIMDPDPFQ.CVIPNFIQCQTFLEGLQKELLDLDFHEKCNDLYKFKQ.DDLKNRDELHIS..RK
Retrocopy RFSHEAIIMDPDPFQYCVIPNFIQCQTFLEGLQKELLDLDFHEKCNDLYKFKQLDDLKNRDELHISV*RK

Parental  VLFEDFRRWLSDIVLIDLESTVDISCAKYEYTDILLCHDDELEGRRIAFILYLVPAWDKSLGGTLDLYST
          VLFE.F.R.LSDIVLIDLESTVDIS.AKY.YTDI.L.HDDELEGRRIAFILYLV..WDKSLGGTLDLYST
Retrocopy VLFEYFWR*LSDIVLIDLESTVDISYAKY*YTDIPLFHDDELEGRRIAFILYLVLPWDKSLGGTLDLYST

Parental  DEHVQPEQIVKSLVPSWNTLVFFEVSPVSYHQVSEVLSEGKCRLSISGWFHGPSQTRSSSYFEPLLPRSP
          DEH.Q.EQ.VKSLVPSWNTLVFFEVS.VS.HQVS.VL.EGKC.LSISGWF.GPSQTRSSSYFEPLLP.SP
Retrocopy DEHFQSEQTVKSLVPSWNTLVFFEVSQVS*HQVS*VLFEGKCQLSISGWFRGPSQTRSSSYFEPLLPCSP

Parental  HILRDNEILYEWINPIYMDIDFQAQIQEEFEERSEILLKEFFKSEKYEKIYEALEKEDLEWSKRGPPNKR
          HILRDNEILYEWINPIYMDID.QAQIQE.FEE.SEILLKEFFK.EKYEKI.EALEKEDLEWSKRGPPNKR
Retrocopy HILRDNEILYEWINPIYMDIDSQAQIQEDFEECSEILLKEFFKYEKYEKICEALEKEDLEWSKRGPPNKR

Parental  FYETAEEEKLPDILRECMELFRSEALFLLLSNFTGLKLHFLVSSDEDDENQTNNDEEESEEISHGSSKGE
          FYETA.EEKLPDILRECMELF.SE.LFLLLSNFTGLKLHFLVSSDEDDE.QT.NDEEESEEISHG.SK.E
Retrocopy FYETAKEEKLPDILRECMELFCSEVLFLLLSNFTGLKLHFLVSSDEDDEDQTDNDEEESEEISHGPSKQE

Parental  NYQEASGHTSQQSKIETALESEDGEAKNKSTVPTCTGELRYWKNGHYTLVHDTKNTEFALDLLFYCGCKG
          NYQEASGHTSQQSKIETALESE..EAKNKS.VPTCTGELRYWKN.HYTLVHDTKNTEFALDLLFYCGCKG
Retrocopy NYQEASGHTSQQSKIETALESENEEAKNKSAVPTCTGELRYWKNVHYTLVHDTKNTEFALDLLFYCGCKG

Parental  WKTEYGGFTSYIAKDEDEELLTVTPEENSLALVYRDRETLKFVKHINHQSLERKKTGQNRTGFWDFSFVY
          WKTEYGGFTSY.AK.EDEELL.VTPEENSLALVYRD.ETLKF.KHINHQ.LE.KKTGQNRTGFWDFSFVY
Retrocopy WKTEYGGFTSYTAKGEDEELLIVTPEENSLALVYRD*ETLKFIKHINHQHLEQKKTGQNRTGFWDFSFVY

Parental  YE
          YE
Retrocopy YE

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	30.99 RPM
SRP007412_cerebellum	0.00 RPM	21.22 RPM
SRP007412_heart	0.00 RPM	44.85 RPM
SRP007412_kidney	0.00 RPM	42.14 RPM
SRP007412_liver	0.00 RPM	63.44 RPM
SRP007412_testis	0.00 RPM	36.14 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_777 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_777 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013378	1 retrocopy	retro_mdom_777 ,
Otolemur garnettii	ENSOGAG00000014894	1 retrocopy	retro_ogar_2808,
Ochotona princeps	ENSOPRG00000006697	1 retrocopy	retro_opri_1103,