RetrogeneDB ID: retro_mdom_1390

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:264519448..264519766(-)
• Located in intron of: ENSMODG00000028613

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC4
• Ensembl ID: ENSMODG00000005136
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 4, 20kDa [Source:HGNC Symbol;Acc:707]

Sequence

>retro_mdom_1390
CTGATTGAGGATTCCATCAACTCTGTTAGAGTCAGCATTGCTGTGAAACAGGCTGATGAGATGGAGAAGATCCTTTGCCA
CAAGTTCATGGGCTTCATGATGATGAGAGCAGAGAACTTCTTCATCTTGTGCAGGAAGCCTGTGGAGGGTTATGATATCA
GTTTCCTGATCACAAAGTTTCATACAGAGCAAATGTACAAACACAAACTGGTGGACTTTGTGATCCACTTCATGGAGGAG
ATTGACAAGGCGATCAGTGAAATGAAGCTGTAGGTCAATGCTCCTGCTCGTATTGTGGCAGAGGAGTTCCTCAAGAAT

Alignment

ORF - retro_mdom_1390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.45 %
• Parental protein coverage: 63.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITNFHTEQMYKHKL
          LIE.SINSVRVSIAVKQADE.EKILCHKFM.FMMMRAENFFIL.RKPVEGYDISFLIT.FHTEQMYKHKL
Retrocopy LIEDSINSVRVSIAVKQADEMEKILCHKFMGFMMMRAENFFILCRKPVEGYDISFLITKFHTEQMYKHKL

Parental  VDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKN
          VDFVIHFMEEIDK.ISEMKL.VNA.ARIVAEEFLKN
Retrocopy VDFVIHFMEEIDKAISEMKL*VNAPARIVAEEFLKN

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_1390 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1390 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007964	2 retrocopies	retro_btau_680, retro_btau_849,
Callithrix jacchus	ENSCJAG00000016175	1 retrocopy	retro_cjac_1681,
Myotis lucifugus	ENSMLUG00000025088	1 retrocopy	retro_mluc_2078,
Monodelphis domestica	ENSMODG00000005136	1 retrocopy	retro_mdom_1390 ,
Otolemur garnettii	ENSOGAG00000026074	2 retrocopies	retro_ogar_1033, retro_ogar_875,