RetrogeneDB ID: retro_mdom_785

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:481425848..481426326(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM162A
• Ensembl ID: ENSMODG00000018300
• Aliases: None
• Description: family with sequence similarity 162, member A [Source:HGNC Symbol;Acc:17865]

Sequence

>retro_mdom_785
ATGGGGAGCATCCGTGGCCTATACCTGGCGGCGGGAAACCATCTGAGGTTATGTGAGAGACAAGTTCTCCCTTCTTTCAG
CCTAGCCAGAAAAGGAGGTTTGAAGATGACGAGAGGATTTTGTTCAAAACCACAAGAATCAAAAGCATCATCTCAGTGTG
CAGATATTTATAAAACTAGAGTGCCATTACATAAGCCCACTCCCTTGGGAAAAGAAGATAATGGTCTGGTCAGGCCGTTT
CAAAAAGGAAGATGAAATTCCAGAGACAATCTCGTTTGAGATGCTTGATGCTGCCAAAAACAGGTTTCGAGTCAGGGTCA
GTTACCTCATGATTGCCCTAACAATCCTGGGATGTGTGATTATGGTTATTCAGGGAAAACAGGCTGTCAAAAGACATGAG
ACCCTGACAAGTCTGAACTTAGAAAGGAAAGCTCTTTTGAGAAAGCAAGAAGAAGAGGCCATCAAGTCCAAAACTGAT

Alignment

ORF - retro_mdom_785 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.12 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGSIRGLYLAAGNHLRLCERQVFPSFSLARKGGLKMTRGFCSKPQESKASSQRADIYKTRVPLHKPT-PW
          MGSIRGLYLAAGNHLRLCERQV.PSFSLARKGGLKMTRGFCSKPQESKASSQ.ADIYKTRVPLHKPT.PW
Retrocopy MGSIRGLYLAAGNHLRLCERQVLPSFSLARKGGLKMTRGFCSKPQESKASSQCADIYKTRVPLHKPT>PW

Parental  EKKIMVWSGRFKKEDEIPETISFEMLDAAKNRFRVRVSYLMIALTILGCVIMVIQGKQAVKRHETLTSLN
          EKKIMVWSGRFKKEDEIPETISFEMLDAAKNRFRVRVSYLMIALTILGCVIMVIQGKQAVKRHETLTSLN
Retrocopy EKKIMVWSGRFKKEDEIPETISFEMLDAAKNRFRVRVSYLMIALTILGCVIMVIQGKQAVKRHETLTSLN

Parental  LERKALLRKQEEEAIKSKTD
          LERKALLRKQEEEAIKSKTD
Retrocopy LERKALLRKQEEEAIKSKTD

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_785 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_785 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014316	1 retrocopy	retro_amel_1533,
Monodelphis domestica	ENSMODG00000018300	1 retrocopy	retro_mdom_785 ,
Mustela putorius furo	ENSMPUG00000004773	1 retrocopy	retro_mputfur_1616,
Otolemur garnettii	ENSOGAG00000003194	1 retrocopy	retro_ogar_2064,
Rattus norvegicus	ENSRNOG00000002255	2 retrocopies	retro_rnor_2587, retro_rnor_337,
Tursiops truncatus	ENSTTRG00000013401	1 retrocopy	retro_ttru_791,