RetrogeneDB ID: retro_mdom_1035

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:305758560..305759679(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC3
• Ensembl ID: ENSMODG00000019911
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 3 [Source:HGNC Symbol;Acc:9549]

Sequence

>retro_mdom_1035
GCTATGAAGGATAAAATCAAAGAGAACACGCTGTAGAAAATTAAAGTGAACAAGACGCTGCCCTACCTTGTTTCCAACGT
TATCGAGCTGCTAGATGTTGACCCCAATGACCAAGAAGAAGATGGTGCAAACATTGACCTTGACTCTCAGAGAAAGGGCA
AATGTGCTGTGATCAAAACCTCTACCCGACAGACCTATTTCCTGCCAGTTATTGGTTTGGTTGATGCAGAGAAATTGAAG
CCGGGAGACCTGGTGGGAGTAAACAAAGATTCCTATCTGATCTTAGAGACCCTGCCCATCGAATATGATTCCCGAGTGAA
GACCATGGAGGTGGATGAGAGGCCCACAGAGCAATACAGTGACATTGGAGGACTGGACAAACAAATCCAGGAACTGGTAG
AGGCTATTGTATTGCCAATGAACCATAAAGAGAAATTTGAGAATTTGGGTATTCAGCTTCCAAAGGGAGTATTGATGTAT
GGACCCCCAGGTACTGGAAAAACCCTGCTAGCCCGTGCATGTGCTGCTCAGACCAAGGCCACCTTTCTGAAATTGGCTGG
ACCCCAGCTGGTACAAATGTTCATTGGGGATGGAGCAAAGCTTGTCCGAGATGCCTTTGCATTGGCTAAAGAGAAAGCTC
CCTCCATTATCTTCATTGATGAGCTGGATGCTATTGGAACCAAACGCTTTGACAGTGAGAAAGCAGGAGATCGTGAAGTT
CAGAGGACAATGCTGGAGCTCTTGAACCAGCTGGATGGATTTCAGCCTAACACTCAAGTCAAGGTGATTGCTGCCACAAA
TAGGGTGGACATCCTAGACCCTGCTTTGCTCCGCTCTGGTCGTCTGGACCGCAAGATTGAATTTCCAATGCCGAATGAGG
AAGCTAGAGCCAGGATCATGCAGATACATTCCCGAAAAATGAATGTGAGCTCTGACGTGAACTATGAGGAGCTAGCACGC
TGTACCAATGATTTCAATGGCGCCCAGTGTAAAGCTGTGTGTGTGGAAGCCGGAATGATCGCCCTCCGGGGTGGAGCCAC
TGAACTCACCCATGAAGACTACATGGAGGGCATCCTGGAGGTTCAGGCCAAGAAGAAAGCCAATTTGCAGTACTATGCT

Alignment

ORF - retro_mdom_1035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.59 %
• Parental protein coverage: 82.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AMKDKIKENSE-KIKVNKTLPYLVSNVIELLDVDPNDQEEDGANIDLDSQRKGKCAVIKTSTRQTYFLPV
          AMKDKIKEN...KIKVNKTLPYLVSNVIELLDVDPNDQEEDGANIDLDSQRKGKCAVIKTSTRQTYFLPV
Retrocopy AMKDKIKENTL*KIKVNKTLPYLVSNVIELLDVDPNDQEEDGANIDLDSQRKGKCAVIKTSTRQTYFLPV

Parental  IGLVDAEKLKPGDLVGVNKDSYLILETLPTEYDSRVKAMEVDERPTEQYSDIGGLDKQIQELVEAIVLPM
          IGLVDAEKLKPGDLVGVNKDSYLILETLP.EYDSRVK.MEVDERPTEQYSDIGGLDKQIQELVEAIVLPM
Retrocopy IGLVDAEKLKPGDLVGVNKDSYLILETLPIEYDSRVKTMEVDERPTEQYSDIGGLDKQIQELVEAIVLPM

Parental  NHKEKFENLGIQPPKGVLMYGPPGTGKTLLARACAAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAK
          NHKEKFENLGIQ.PKGVLMYGPPGTGKTLLARACAAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAK
Retrocopy NHKEKFENLGIQLPKGVLMYGPPGTGKTLLARACAAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAK

Parental  EKAPSIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSG
          EKAPSIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSG
Retrocopy EKAPSIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSG

Parental  RLDRKIEFPMPNEEARARIMQIHSRKMNVSPDVNYEELARCTDDFNGAQCKAVCVEAGMIALRRGATELT
          RLDRKIEFPMPNEEARARIMQIHSRKMNVS.DVNYEELARCT.DFNGAQCKAVCVEAGMIALR.GATELT
Retrocopy RLDRKIEFPMPNEEARARIMQIHSRKMNVSSDVNYEELARCTNDFNGAQCKAVCVEAGMIALRGGATELT

Parental  HEDYMEGILEVQAKKKANLQYYA
          HEDYMEGILEVQAKKKANLQYYA
Retrocopy HEDYMEGILEVQAKKKANLQYYA

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_1035 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1035 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008701	1 retrocopy	retro_cfam_52,
Monodelphis domestica	ENSMODG00000019911	2 retrocopies	retro_mdom_1035 , retro_mdom_1540,
Mustela putorius furo	ENSMPUG00000003992	1 retrocopy	retro_mputfur_1487,