RetrogeneDB ID: retro_mdom_1497

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:22112530..22112989(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPRYD7
• Ensembl ID: ENSMODG00000010799
• Aliases: None
• Description: SPRY domain containing 7 [Source:HGNC Symbol;Acc:14297]

Sequence

>retro_mdom_1497
AAAAATGGAAGAAGAATATGTGGGACAGGAGGTTGTTTAGCTAATGCACCTTTGCATCAGAACAAAAGCTATTTCGAATT
TAAAATCCAATCCACAGGGATTTGGGGCATTGGAGTGGCAACACAGAAAGTTAATTTGAATCAGATTCCTCTTGGCCAAG
ATGTTCATAGCCTTGTGATGAGGAATGATGGAGCTCTCTATCACAACAATGAGGAAAAGAATAGGCTGCTAGGAAATAAT
CTTCCACAGGAAGGAGATGTACTGGGTATTACGTATGACCATGTAGAATTAAATGTGTATTTGAATGGAAAGAATATGCA
CTGTCCAGCATCAGGTATATGAGGGACAGTGTATCCTGTTGTATATGTTGATGACAGTGAGATTTTGGATTGCCAATTCA
GTGACTTTTATCATATTCCTCCAACTGGTTTTGAAAAAATATTATTTGAACAGCAGATC

Alignment

ORF - retro_mdom_1497 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.08 %
• Parental protein coverage: 88.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNGRRICGTGGCLANAPLHQNKSYFEFKIQSTGIWGIGVATQKVNLNQIPLGRDVHSLVMRNDGALYHNN
          KNGRRICGTGGCLANAPLHQNKSYFEFKIQSTGIWGIGVATQKVNLNQIPLG.DVHSLVMRNDGALYHNN
Retrocopy KNGRRICGTGGCLANAPLHQNKSYFEFKIQSTGIWGIGVATQKVNLNQIPLGQDVHSLVMRNDGALYHNN

Parental  EEKNRLPANNLPQEGDVVGITYDHVELNVYLNGKNMHCPASGIRGTVYPVVYVDDSAILDCQFSDFYHIP
          EEKNRL..NNLPQEGDV.GITYDHVELNVYLNGKNMHCPASGI.GTVYPVVYVDDS.ILDCQFSDFYHIP
Retrocopy EEKNRLLGNNLPQEGDVLGITYDHVELNVYLNGKNMHCPASGI*GTVYPVVYVDDSEILDCQFSDFYHIP

Parental  PTGFEKILFEQQI
          PTGFEKILFEQQI
Retrocopy PTGFEKILFEQQI

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_1497 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1497 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011472	1 retrocopy	retro_ecab_179,
Monodelphis domestica	ENSMODG00000010799	2 retrocopies	retro_mdom_1497 , retro_mdom_613,
Mus musculus	ENSMUSG00000021930	1 retrocopy	retro_mmus_3095,
Rattus norvegicus	ENSRNOG00000015095	1 retrocopy	retro_rnor_1652,
Tarsius syrichta	ENSTSYG00000007075	1 retrocopy	retro_tsyr_791,