RetrogeneDB ID: retro_mdom_1571

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:11991539..11992742(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1M2
• Ensembl ID: ENSMODG00000005838
• Aliases: None
• Description: adaptor-related protein complex 1, mu 2 subunit [Source:HGNC Symbol;Acc:558]

Sequence

>retro_mdom_1571
CAGCCCCTGATCTGCCAGAACTACAAGGGGGATGTGAGCATGGCCAAGATTGACTACTTCATTCCCCTGCAGAAGGAAGA
AGAGGGAGCCCTGACCCCACTGCTGACCCATGGCAAGGTGCACTTCCTGTTGATCAAATATAGCAAACTTTACTTGGTGG
CTACCACCCTCAAGAATGCCAATGCCTCTCTGGTGTACTCTTTTCTCTACAAGGCTGTTGAGGTTTTCTTTGAGTATTTC
AAGGAACTAGAGGAAGAGAGCATGCATCCCAGACAATTTCGTCATTGTCTATGAACTATTGGATGAGCTCATGGATTCTG
GCTTTCCACAAACCATGGACAGCAAAATTCTCCTGGAGTATATCACCCAGCAGGGCAACAAATTAGAGACAGGCAAGTCC
CGAGTGCCCCCAACAGTTACCAATGGTGTGTCTTGGCATTCTGAGTATATCAAATATAAGAAAATGAGGTTTTTCATTGA
TGTTATTGAGTCTGTCAACCTACTGGTCAATGCCAATGGGACTGTGCTGCTGAGTGAGATTGTGGACACCATTAAGCTGA
AGGTGTTCTTGTCTAGCATGCCAGAGCTGAGATTGGGACTCAATAACCGGGTACTTTTTGAACTCACTGGCCGAAATAAA
AACAAGTCTGTTGAATTGGAAGATGTTAAGTTCCATCAGTGTGTACGACTTTCTAGATTTGACAATGATTGAACCATCTC
CATCATCCCACCTGATGGTGACTTTGAACTTATGTCCTATTGGCTCAATACCCAGGGAAAACTACTGATATGGATTGAGT
CTATCATTGAAAAGTTCTCACACAGTAGGGTAGAAATTATGGTTAAGGCTAAAGGCCAGTTTAAGAAGCAGTCAGTGGCC
AAGAGTGTGGAGATTGTAGTCCCAGTGCACAGTGATGCAGATTTCTCCTGATTCAAAACCAGTGTGGGCAGCACCAAGTA
CCTGCCTGAGAAAAATGTGTTTATCTGGAACATCAAGTCCTTTCCTGGAGGAAAGGAATACCTAATGAGAGTACACTTTG
GCTTGCCTGCCTGGAGAAAGAGGAAGTGGAGAGCTGGCCTCCCATCTCTGTCAAATTTGAGATTCCTTATTTTACTGTCT
CTGGGATACAGGTATGGTACATGAAGATCATTGAGAAGAGTGGGTACCAAGCTCTTCCTTGGGTTCAACATATCACCCAG
AGT

Alignment

ORF - retro_mdom_1571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.24 %
• Parental protein coverage: 95.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KPLICRNYKGDVSMTEIDHFMPLLMQKEEEGALTPLLTHGRVHFLWIKYSNLYLVATTLKNANASLVYSF
          .PLIC.NYKGDVSM..ID.F.PL..QKEEEGALTPLLTHG.VHFL.IKYS.LYLVATTLKNANASLVYSF
Retrocopy QPLICQNYKGDVSMAKIDYFIPL--QKEEEGALTPLLTHGKVHFLLIKYSKLYLVATTLKNANASLVYSF

Parental  LYKAVEVFSEYFKEL-EEES-IRDNFVIVYELLDELMDFGFPQTTDSKILQEYITQQGNKLETGKSRVPP
          LYKAVEVF.EYFKEL.EE...I.DNFVIVYELLDELMD.GFPQT.DSKIL.EYITQQGNKLETGKSRVPP
Retrocopy LYKAVEVFFEYFKELEEESM>IPDNFVIVYELLDELMDSGFPQTMDSKILLEYITQQGNKLETGKSRVPP

Parental  TVTNAVSWRSEGIKYKKNEVFIDVIESVNLLVNANGSVLLSEIVGTIKLKVFLSGMPELRLGLNDRVLFE
          TVTN.VSW.SE.IKYKK...FIDVIESVNLLVNANG.VLLSEIV.TIKLKVFLS.MPELRLGLN.RVLFE
Retrocopy TVTNGVSWHSEYIKYKKMRFFIDVIESVNLLVNANGTVLLSEIVDTIKLKVFLSSMPELRLGLNNRVLFE

Parental  LTGLSGNKNKSVELEDVKFHQCVRLSRFDNDRTISFIPPDGDFELMSYRLNTQVKPLIWIESVIEKFSHS
          LTG...NKNKSVELEDVKFHQCVRLSRFDND.TIS.IPPDGDFELMSY.LNTQ.K.LIWIES.IEKFSHS
Retrocopy LTGR--NKNKSVELEDVKFHQCVRLSRFDND*TISIIPPDGDFELMSYWLNTQGKLLIWIESIIEKFSHS

Parental  RVEIMVKAKGQFKKQSVANSVEIAVPVPSDADSPRFKTSVGSAKYLPEKNVVIWNIKSFPGGKEYLMRAH
          RVEIMVKAKGQFKKQSVA.SVEI.VPV.SDAD...FKTSVGS.KYLPEKNV.IWNIKSFPGGKEYLMR.H
Retrocopy RVEIMVKAKGQFKKQSVAKSVEIVVPVHSDADFS*FKTSVGSTKYLPEKNVFIWNIKSFPGGKEYLMRVH

Parental  FGLPS-VEKEEVEGRPPISVKFEIPYFTVSGIQVRYMKIIEKSGYQALPWVRYITQS
          FGLP...EKEEVE..PPISVKFEIPYFTVSGIQV.YMKIIEKSGYQALPWV..ITQS
Retrocopy FGLPA<LEKEEVESWPPISVKFEIPYFTVSGIQVWYMKIIEKSGYQALPWVQHITQS

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_1571 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1571 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000003643	1 retrocopy	retro_meug_1894,
Monodelphis domestica	ENSMODG00000000660	1 retrocopy	retro_mdom_1564,
Monodelphis domestica	ENSMODG00000005838	2 retrocopies	retro_mdom_1571 , retro_mdom_451,
Ornithorhynchus anatinus	ENSOANG00000010455	1 retrocopy	retro_oana_88,
Oryctolagus cuniculus	ENSOCUG00000024334	1 retrocopy	retro_ocun_1089,