RetrogeneDB ID: retro_mdom_451

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:611657719..611658697(+)
• 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_451
TATTCTCAGTATTTTAAGGAACTAGAGGAAGAGAGTATCTGAGACAATTTCATCATTGTCTATGAGGTATTGGATGAGCT
CATGGATTTTGGCTTTTCACAAACCATGAACAGAAAAATTCTCCAAGAGTATATCACCCAGCAGGACAACAAATAAGAGA
CAGACAAGTCCTGGGTGCCCCCAACAGTTGCCAATGCTGTGTCTTGGCGTTCATAGGGTATCAAATATAAGAAGAACAAT
GTTTTCATTGATGTTATTGAGTCTGTCAACTGACTGGTCAATGCCAATGGGAGTGTGCAGCTGACTGAGATTGTGGGCAC
CATCAAGCTAAAGGGGTTCTTGTCTGGCATGCCAGAGCTGAGATTGGGAATTAATGACCGGGTACTTTTTGAACTCACTG
GCTGCAATAAAAACAAGTCTGTTGAATTGGAAGATGTTAAGGTCCATCAGTGTGTACAACTCTCTAGATTTGACAATGAT
CGAATCATCTCCTTTATCCCACCTGATGGTGACTTTGAACTTATGTCCTATCGGTTCAATGCCTAGATAAAACCACTGAT
ATGGATTGAGTCTGTCATTGAAAAGTTTTCACACAGTTGGGTGGAAATTATGGTTAAGGCTAAAGGCCAGTTAAAGAAGC
AGCCAGTGGACAACAGTGTGGAGATCACAGTCCCAGTGCCCAGTGATGAAGATTCCCCCCGATTCAAAACCAGTGTGGGG
AATGCCAAGTACCTGCCTGAGAACAATGTGGTTATCTGGAACATCAAGTCCTTTCCTGGAGGAAAGGAATACCTAATGAG
ATCACACTTTGGCTTGCCTAGGGTAGAGAAAGAGGAAGTGGAGGGCTGGCCTCCCATCTCTGTCAAATTTGAGATTCATT
ATTTTACTGTCTCTGGGATCCAGGTCCGGTACATGAAGATCATTGAGAAGAGTGGGTACCAAGTTCTTACTTGGGTTCCA
TATATCACCCAAAGTGGG

Alignment

ORF - retro_mdom_451 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.98 %
• Parental protein coverage: 77.18 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FSEYFKELEEESIRDNFVIVYELLDELMDFGFPQTTDSKILQEYITQQGNKLETGKSRVPPTVTNAVSWR
          .S.YFKELEEESI.DNF.IVYE.LDELMDFGF.QT...KILQEYITQQ.NK.ET.KS.VPPTV.NAVSWR
Retrocopy YSQYFKELEEESI*DNFIIVYEVLDELMDFGFSQTMNRKILQEYITQQDNK*ETDKSWVPPTVANAVSWR

Parental  SEGIKYKKNEVFIDVIESVNLLVNANGSVLLSEIVGTIKLKVFLSGMPELRLGLNDRVLFELTGLSGNKN
          S.GIKYKKN.VFIDVIESVN.LVNANGSV.L.EIVGTIKLK.FLSGMPELRLG.NDRVLFELTG...NKN
Retrocopy S*GIKYKKNNVFIDVIESVN*LVNANGSVQLTEIVGTIKLKGFLSGMPELRLGINDRVLFELTGC--NKN

Parental  KSVELEDVKFHQCVRLSRFDNDRTISFIPPDGDFELMSYRLNTQVKPLIWIESVIEKFSHSRVEIMVKAK
          KSVELEDVK.HQCV.LSRFDNDR.ISFIPPDGDFELMSYR.N...KPLIWIESVIEKFSHS.VEIMVKAK
Retrocopy KSVELEDVKVHQCVQLSRFDNDRIISFIPPDGDFELMSYRFNA*IKPLIWIESVIEKFSHSWVEIMVKAK

Parental  GQFKKQSVANSVEIAVPVPSDADSPRFKTSVGSAKYLPEKNVVIWNIKSFPGGKEYLMRAHFGLPSVEKE
          GQ.KKQ.V.NSVEI.VPVPSD.DSPRFKTSVG.AKYLPE.NVVIWNIKSFPGGKEYLMR.HFGLP.VEKE
Retrocopy GQLKKQPVDNSVEITVPVPSDEDSPRFKTSVGNAKYLPENNVVIWNIKSFPGGKEYLMRSHFGLPRVEKE

Parental  EVEGRPPISVKFEIPYFTVSGIQVRYMKIIEKSGYQALPWVRYITQSG
          EVEG.PPISVKFEI.YFTVSGIQVRYMKIIEKSGYQ.L.WV.YITQSG
Retrocopy EVEGWPPISVKFEIHYFTVSGIQVRYMKIIEKSGYQVLTWVPYITQSG

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	0.59 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_451 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_451 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,