RetrogeneDB ID: retro_mdom_1681

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:174770131..174770354(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEDD8
• Ensembl ID: ENSMODG00000003254
• Aliases: None
• Description: neural precursor cell expressed, developmentally down-regulated 8 [Source:HGNC Symbol;Acc:7732]

Sequence

>retro_mdom_1681
CTGACAGGAAAAGAAATTGAGAATTGACACTGAATCCATAGGCAAGGTAGAATGGATCAAAGAGCGGGTGGAAGAAAAAG
AGGGAATTCCTCTATAGCCGCAACAACTCATCTACAGTGGTAAACAGATGAAAGACTAGAAAACAGGCTCTGATTCCAAG
ATCCAGGGACATTCAGTACTCCATTTGCTGTTCGCTCTTTGTGGGGGAGGAGATCTTGGGCGG

Alignment

ORF - retro_mdom_1681 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 91.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTGKEIE-IDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKIQGGSVLHLVLALRGG
          LTGKEIE.ID.E...KVE.IKERVEEKEGIP...Q.LIYSGKQM.D.KT..D.KIQG.SVLHL..AL.GG
Retrocopy LTGKEIE>IDTESIGKVEWIKERVEEKEGIPL*PQQLIYSGKQMKD*KTGSDSKIQGHSVLHLLFALCGG

Parental  GGLGR
          G.LGR
Retrocopy GDLGR

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	204.54 RPM
SRP007412_cerebellum	0.00 RPM	255.94 RPM
SRP007412_heart	0.00 RPM	155.49 RPM
SRP007412_kidney	0.00 RPM	160.65 RPM
SRP007412_liver	0.00 RPM	129.40 RPM
SRP007412_testis	0.00 RPM	167.36 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1681 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1681 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 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038842	1 retrocopy	retro_btau_89,
Canis familiaris	ENSCAFG00000012097	1 retrocopy	retro_cfam_1789,
Choloepus hoffmanni	ENSCHOG00000001228	5 retrocopies	retro_chof_1012, retro_chof_1616, retro_chof_2696, retro_chof_613, retro_chof_788,
Callithrix jacchus	ENSCJAG00000006876	1 retrocopy	retro_cjac_4064,
Cavia porcellus	ENSCPOG00000010930	1 retrocopy	retro_cpor_371,
Erinaceus europaeus	ENSEEUG00000011640	2 retrocopies	retro_eeur_165, retro_eeur_43,
Echinops telfairi	ENSETEG00000018391	2 retrocopies	retro_etel_1118, retro_etel_1677,
Homo sapiens	ENSG00000129559	1 retrocopy	retro_hsap_180,
Gorilla gorilla	ENSGGOG00000016105	1 retrocopy	retro_ggor_261,
Macaca mulatta	ENSMMUG00000029409	1 retrocopy	retro_mmul_2236,
Monodelphis domestica	ENSMODG00000003254	1 retrocopy	retro_mdom_1681 ,
Vicugna pacos	ENSVPAG00000009104	4 retrocopies	retro_vpac_270, retro_vpac_316, retro_vpac_480, retro_vpac_558,