RetrogeneDB ID: retro_mdom_1403

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:313175511..313175837(-)
• Located in intron of: ENSMODG00000028491

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011615
• Aliases: None
• Description: None

Sequence

>retro_mdom_1403
TCTAAAGATAATTTAGCAGCTAAAATTTTATCCTACAATGGAGCAAACTGAGTAGCAGCCATTCTGTTCAACCATCAGTG
GGCGACTCCAAAGACTTTTGAGAAGTCCATGCAAAATCTCCAAGGATTGATACGCAAAAGGAGTAGCTAGCTATGGTAGA
AAGCAAAAAAGAAAGCAAAGACTGATGCCAAAGTGAGAAAGGGTGTCGAGTCCATGAGTAATGTGTAGAAGAATAAAAAA
CTGCTAGCTATGTGAGAAGAATAATTCATTAAGGTTTATGCCCAAGGCACAGCTAAGGAGAAAAAACACAGATAGCCCTG
GGCACC

Alignment

ORF - retro_mdom_1403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.52 %
• Parental protein coverage: 67.68 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEDNIAAKILSYNRANRAVAILCNHQRATPKTFEKSMQNLQTKINAKKEQLA-MAKQELKRAKADAKVKK
          ..DN.AAKILSYN.AN...AIL.NHQ.ATPKTFEKSMQNLQ..I......L...AK...K....DAKV.K
Retrocopy SKDNLAAKILSYNGAN*VAAILFNHQWATPKTFEKSMQNLQGLIRKRSS*LW*KAKKKAK---TDAKVRK

Parental  DVKSESNVDKKKKLLAKLEEQLMRLHTQATDKE-ENKQVALGT
          .V.S.SNV.K.KKLLA..EE.......Q.T.KE.E..Q.ALGT
Retrocopy GVESMSNV*KNKKLLAM*EE*FIKVYAQGTAKE<EKTQIALGT

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_1403 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1403 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000011615	1 retrocopy	retro_mdom_1403 ,