RetrogeneDB ID: retro_mdom_1773

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:53132528..53132809(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FIS1
• Ensembl ID: ENSMODG00000005034
• Aliases: None
• Description: fission 1 (mitochondrial outer membrane) homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21689]

Sequence

>retro_mdom_1773
GTGTCACAAAGTACCCAGTTTTAGTATTCCAGGTTGTCTGGTGTGAAGTAAATGCAACGATATCTGAAAACCCAAAGGGC
TCCAGGAGGAGTTGCTATCTGAAGGGAACAAAGAGGCAATGAGATTATATCCACCACTTGGTTTGCAGGAAACACAACTT
CCTGAAGAAATATGAGAAGGCTCTGAAGTATATGAGAGGATTGATGTGGACTGAATTCTAGAATAACCCAGCCAAGGAGC
TAGGATGTCTCATTGATAAGGTTGTAAGGAAGAATAGTCTT

Alignment

ORF - retro_mdom_1773 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.7 %
• Parental protein coverage: 61.84 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSHSTQFEYA-WCLVRSRYNDDIRKGIGLLEELLS-KGSKEEQRDYVFYLAVGNYR-LKEYEKALKYVRG
          VS.STQF.Y...CLV.S..ND.I.K..GL.EELLS.KG.K..Q.DY...L.......LK.YEKALKY.RG
Retrocopy VSQSTQF*YS>GCLV*SKCND-I*KPKGLQEELLS>KGTKR-Q*DYIHHLVCRKHNFLKKYEKALKYMRG

Parental  LLQTEPQNNQARELECLIDKAMKKDGL
          L..TE..NN.A.EL.CLIDK...K..L
Retrocopy LMWTEF*NNPAKELGCLIDKVVRKNSL

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_1773 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1773 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013800	2 retrocopies	retro_cfam_557, retro_cfam_755,
Callithrix jacchus	ENSCJAG00000016053	1 retrocopy	retro_cjac_1913,
Loxodonta africana	ENSLAFG00000020494	1 retrocopy	retro_lafr_702,
Myotis lucifugus	ENSMLUG00000024207	1 retrocopy	retro_mluc_168,
Monodelphis domestica	ENSMODG00000005034	1 retrocopy	retro_mdom_1773 ,
Otolemur garnettii	ENSOGAG00000028158	1 retrocopy	retro_ogar_1544,
Rattus norvegicus	ENSRNOG00000001420	2 retrocopies	retro_rnor_1659, retro_rnor_1689,
Sus scrofa	ENSSSCG00000027757	1 retrocopy	retro_sscr_1083,