RetrogeneDB ID: retro_mdom_12

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:166400972..166401413(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024949
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005721
• Aliases: None
• Description: None

Sequence

>retro_mdom_12
ATGTCAGCAGAACCTCCCAAACTACTGAAGACCCCCACCCATCCAGCCTCTCTCCGTCTACCTGATGGTGCCCGGGAAAG
GAACTGTTCACCATCTCCTATGAGAGGGTACCTCATCCCTAGCCCTTTGCCAACCCGACGGACTAGGACCTTTTCAGTGA
CTGTTGCATCTGAGGGACCCATCTACAAGGGTGTCTGTAAGTGCTTTTACCGTTCCAAGGGGCATGGCTTCATTACACCA
GCAGATGGTGGCCCTGACATCTTCCTTCTTATCTCTGATGTGGAAGGAGAATACATGCCTATGGAAGGAGATGAAGTCAC
TTACAAGATGTGTTCAATCCCACCCAAGAATGAGAAGCACCAGGCTGTGGAAGTTGTCATCACTCACCTGGCACCAGGCA
CCAAACATGAGACCTGGTCAGGACATGTCATCAGTTCCTAG

Alignment

ORF - retro_mdom_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.88 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSAEPPKPPKAPTHPASLRLPDGARERNRSPSPMRGYLIPSPLPTRRTRTFSATVRASEGPIYKGVCKCF
          MSAEPPK..K.PTHPASLRLPDGARERN.SPSPMRGYLIPSPLPTRRTRTFS.TV.ASEGPIYKGVCKCF
Retrocopy MSAEPPKLLKTPTHPASLRLPDGARERNCSPSPMRGYLIPSPLPTRRTRTFSVTV-ASEGPIYKGVCKCF

Parental  CRSKGHGFITPADGGPDIFLHISDVEGEYVPMEGDEVTYKMCSIPPKNEKHQAVEVVITHLAPGTKHETW
          .RSKGHGFITPADGGPDIFL.ISDVEGEY.PMEGDEVTYKMCSIPPKNEKHQAVEVVITHLAPGTKHETW
Retrocopy YRSKGHGFITPADGGPDIFLLISDVEGEYMPMEGDEVTYKMCSIPPKNEKHQAVEVVITHLAPGTKHETW

Parental  SGHVISS
          SGHVISS
Retrocopy SGHVISS

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_12 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_12 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017286	1 retrocopy	retro_cjac_194,
Macropus eugenii	ENSMEUG00000016403	1 retrocopy	retro_meug_1949,
Monodelphis domestica	ENSMODG00000005721	1 retrocopy	retro_mdom_12 ,
Mus musculus	ENSMUSG00000008393	1 retrocopy	retro_mmus_88,
Rattus norvegicus	ENSRNOG00000002610	1 retrocopy	retro_rnor_1025,