RetrogeneDB ID: retro_mdom_1079

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:15683020..15683347(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5D
• Ensembl ID: ENSMODG00000005314
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit [Source:HGNC Symbol;Acc:837]

Sequence

>retro_mdom_1079
TCAATGAGGCCAATGAAAAGCCCAAACCACAGTGGTACCGTATAGATTTGGACTGCCCAAATCCTTGTGGTGCAGGTACT
AAGGAAGATGTGTCGCTGTGAAGATGGCTTGACCATCAGATATTTTGTGAGTAACGGCTCCAATTCAGTGAATTCCTCTG
TGCAGCTGCCAGCAGAAGAAACCGTGTCCCTGGACAAGCTAGCCATCGCTGCCAAATCGAATTTGGAAAAGATCCACTCA
GATCTGTCAAGAGCCTCAGAAGAGGCACCTCTGACTGAGGTCCAGACATAAATAGAAGTCATTGAAGCTGCTGTGAAAGC
ATGAGAG

Alignment

ORF - retro_mdom_1079 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.3 %
• Parental protein coverage: 66.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVKQVDVPTQSGAFGILAAHVPTLQVLKPGIVTVHAEDGTTTKYFVSSGSITVNADSSVQLLAEEAVSLD
          .......P..SG...I..A.....QVL.........EDG.T..YFVS.GS..VN..SSVQL.AEE.VSLD
Retrocopy SMRPMKSPNHSGTV*IWTAQILVVQVLRK---MCRCEDGLTIRYFVSNGSNSVN--SSVQLPAEETVSLD

Parental  MLDLGAAKSNLEKAHSELSGASDEAARAEAQIRIEANEAIVKALE
          .L...AAKSNLEK.HS.LS.AS.EA...E.Q..IE..EA.VKA.E
Retrocopy KLAI-AAKSNLEKIHSDLSRASEEAPLTEVQT*IEVIEAAVKA*E

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_1079 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1079 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002168	1 retrocopy	retro_acar_96,
Canis familiaris	ENSCAFG00000019536	1 retrocopy	retro_cfam_1372,
Microcebus murinus	ENSMICG00000014960	1 retrocopy	retro_mmur_1137,
Myotis lucifugus	ENSMLUG00000015004	1 retrocopy	retro_mluc_2544,
Monodelphis domestica	ENSMODG00000005314	1 retrocopy	retro_mdom_1079 ,
Rattus norvegicus	ENSRNOG00000014625	1 retrocopy	retro_rnor_1978,