RetrogeneDB ID: retro_mdom_1208

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:493511824..493512352(-)
• Located in intron of: ENSMODG00000012002

Retrocopy information

• Ensembl ID: ENSMODG00000012006
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GID8
• Ensembl ID: ENSMODG00000016835
• Aliases: None
• Description: GID complex subunit 8 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:15857]

Sequence

>retro_mdom_1208
ATGAGTTATGCAGAAAAACCCGATGAAATTACTAAAGATGAGTGGATGGAAAAATTCAATAACTTGCATATACAGAGAGC
TGATATGAGCCTACTCATTATGAACTATCTTGTTACAGAGGGGTTTAAGGAAGCTGCTGAAAAGTTTCCAGTGGAGTCTG
GAATTGAGCCCAGTGTTGATCTAGAAACATTAGATGAGCCAATCAAAATACGAGAGATGATATTGAACGGTCAGATTCAG
GAAGCTATTGCACTGATAAATAGCCTACATCCAGCGTTCTTAGACACAAATCGGTATCTTTATTTTCATTTACAGCAACA
ACATTTGATTGAACTGATTCGGCAGCGTGAAACAGAAGCAGCCTTGAAATTTGCACAAACACAGTTAGCGGAACAAGGAG
AAGAAAGTAGAGAGTGCCTGACAGAAATGGAACGCACCTTGGCTTTGCTTGCCTTTGATAATCCTCAAGAATCACTCTTT
GGAGATTTGCTTAACATGATGCAACGGCACAAGGGGTGGAGTGAAGTT

Alignment

ORF - retro_mdom_1208 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.05 %
• Parental protein coverage: 77.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYAEKPDEITKDEWMEKLNNLHIQRADMNRLIMNYLVTEGFKEAAEKFRMESGIEPSVDLETLDERIKI
          MSYAEKPDEITKDEWMEK.NNLHIQRADM..LIMNYLVTEGFKEAAEKF..ESGIEPSVDLETLDE.IKI
Retrocopy MSYAEKPDEITKDEWMEKFNNLHIQRADMSLLIMNYLVTEGFKEAAEKFPVESGIEPSVDLETLDEPIKI

Parental  REMILKGQIQEAIALINSLHPELLDTNRYLYFHLQQQHLIELIRQRETEAALEFAQTQLAEQGEESRECL
          REMIL.GQIQEAIALINSLHP..LDTNRYLYFHLQQQHLIELIRQRETEAAL.FAQTQLAEQGEESRECL
Retrocopy REMILNGQIQEAIALINSLHPAFLDTNRYLYFHLQQQHLIELIRQRETEAALKFAQTQLAEQGEESRECL

Parental  TEMERTLALLAFDNPEESPFGDLLNMMQRQKVWSEV
          TEMERTLALLAFDNP.ES.FGDLLNMMQR.K.WSEV
Retrocopy TEMERTLALLAFDNPQESLFGDLLNMMQRHKGWSEV

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	150.43 RPM
SRP007412_cerebellum	0.00 RPM	120.14 RPM
SRP007412_heart	0.00 RPM	47.45 RPM
SRP007412_kidney	0.00 RPM	119.83 RPM
SRP007412_liver	0.00 RPM	117.82 RPM
SRP007412_testis	0.00 RPM	183.67 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1208 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1208 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012749	1 retrocopy	retro_cfam_1551,
Myotis lucifugus	ENSMLUG00000016381	2 retrocopies	retro_mluc_417, retro_mluc_418,
Monodelphis domestica	ENSMODG00000016835	1 retrocopy	retro_mdom_1208 ,
Mus musculus	ENSMUSG00000027573	1 retrocopy	retro_mmus_1267,
Otolemur garnettii	ENSOGAG00000013834	1 retrocopy	retro_ogar_2550,
Rattus norvegicus	ENSRNOG00000010180	1 retrocopy	retro_rnor_2248,
Sorex araneus	ENSSARG00000013102	2 retrocopies	retro_sara_396, retro_sara_598,