RetrogeneDB ID: retro_mdom_1030

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:297044912..297045284(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTZ1
• Ensembl ID: ENSMODG00000005427
• Aliases: None
• Description: glutathione S-transferase zeta 1 [Source:HGNC Symbol;Acc:4643]

Sequence

>retro_mdom_1030
GACCCCAAGGAAAGGGCCAGTGTCTGCATGATCTTGGACCTCATTGCTAGTGGAATTTGGCCCCTGCAAAACTTATCTAT
CCTAAAGAAATTGGGTCAAGAAACTCAGCTGACATGGGCACAAGCAGTCATCAGCTCTGGCTTTAGAGCCCTAGAGAGTG
TCCTACAGAGCACAAAAGGGAAGTATTGCCTGGGAAATTAGATCTCCATGGCTGACTTATGTCTGGTGCCTCCAAGGGCT
AATGCTGAAAGATAGAATGTGGTCCTCTCCCTATACCCCACCATCATGTGCACTTACAAGACCTTGCTCACCATAGAGCA
TTTCCAAGTGAGCCATCCTTCTCAGCAGCCTGACACCCCTCCAGAACTTCGA

Alignment

ORF - retro_mdom_1030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.87 %
• Parental protein coverage: 54.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DPKERASVRMISDLIASGIQPLQNLSILKKVGQETQLAWAQAVISSGFKALESVLQSTAGKYCLGNEISM
          DPKERASV.MI.DLIASGI.PLQNLSILKK.GQETQL.WAQAVISSGF.ALESVLQST.GKYCLGN.ISM
Retrocopy DPKERASVCMILDLIASGIWPLQNLSILKKLGQETQLTWAQAVISSGFRALESVLQSTKGKYCLGN*ISM

Parental  ADLCLVPQVANAERYKVDLSPYPTITRIYKTLLTVEAFQVSHPSRQPDTPPELR
          ADLCLVP..ANAER..V.LS.YPTI...YKTLLT.E.FQVSHPS.QPDTPPELR
Retrocopy ADLCLVPPRANAER*NVVLSLYPTIMCTYKTLLTIEHFQVSHPSQQPDTPPELR

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	73.19 RPM
SRP007412_cerebellum	0.00 RPM	58.76 RPM
SRP007412_heart	0.00 RPM	246.20 RPM
SRP007412_kidney	0.00 RPM	1934.43 RPM
SRP007412_liver	0.00 RPM	2050.21 RPM
SRP007412_testis	0.00 RPM	48.52 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1030 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1030 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017287	1 retrocopy	retro_dnov_116,
Monodelphis domestica	ENSMODG00000005427	1 retrocopy	retro_mdom_1030 ,
Xenopus tropicalis	ENSXETG00000011079	1 retrocopy	retro_xtro_38,