RetrogeneDB ID: retro_mdom_1394

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:272728554..272728773(-)
• Located in intron of: ENSMODG00000004022

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2H
• Ensembl ID: ENSMODG00000002570
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide H [Source:HGNC Symbol;Acc:9195]

Sequence

>retro_mdom_1394
AAGAAGTTTGATTGAATGTCCCTGTTGCCCTGTGAAGGGAAAATGGACCTTATTTTAAAAGTTAATATCCAGATATAACC
TGTAGACTTTGGTGACAAGTTTGAGTTTGTGATAGCCAGTATCTTGATGAGACTGGGTGGCAGGAAGAACAATCCCACAG
ATGATCAGCTATTCAGGGCTGACCAATTTGAGGATGCAATGACTGGCGAAGCTCACAGA

Alignment

ORF - retro_mdom_1394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.23 %
• Parental protein coverage: 52.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTDDRPSRADQFE
          KKFD..S.L.CE....KMDLIL.VNIQI.PVD.GDKF..VIAS.L.....L.....NPTDD...RADQFE
Retrocopy KKFD*MSLLPCEG---KMDLILKVNIQI*PVDFGDKFEFVIASILMR---LGGRKNNPTDDQLFRADQFE

Parental  YVMYGKVYR
          ..M.G...R
Retrocopy DAMTGEAHR

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_1394 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1394 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005751	1 retrocopy	retro_dnov_709,
Microcebus murinus	ENSMICG00000011294	1 retrocopy	retro_mmur_537,
Myotis lucifugus	ENSMLUG00000022295	2 retrocopies	retro_mluc_2322, retro_mluc_552,
Monodelphis domestica	ENSMODG00000002570	2 retrocopies	retro_mdom_1394 , retro_mdom_1450,
Mus musculus	ENSMUSG00000021018	2 retrocopies	retro_mmus_3549, retro_mmus_936,
Otolemur garnettii	ENSOGAG00000001599	1 retrocopy	retro_ogar_3073,
Rattus norvegicus	ENSRNOG00000001748	2 retrocopies	retro_rnor_1377, retro_rnor_773,