RetrogeneDB ID: retro_mdom_1813

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:197379690..197380397(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTFR2
• Ensembl ID: ENSMODG00000017453
• Aliases: None
• Description: mitochondrial fission regulator 2 [Source:HGNC Symbol;Acc:21115]

Sequence

>retro_mdom_1813
AGACAGCTCCTGGAATACTTAGGCTTCCCCTGAGAACAGTTTACACCAATATGGGAAGCTCACACAAATGGTCGAAGTAT
TGTTCGAGTTATAGTGACAAATTTACCTTCAAATCTTTTTTCAAGAACTGATTTGTACCAGATATGTTCCACTATTTTAC
CATCATGGGAAAATAAGGAATATGGATCTACTTGAAGTATTGTTCATAGCATTGGGAACATTTTACCTTTAGAACATTGT
CCAAGGCCGAACTGTGAGCTGTTCCAATACATGAAGTCTTTAGACTATGATCAACATGGATCTGCTCAGAGTCCCATAGT
TCCATTATTTGCTGATATCCTATGTGTGCCAAATGATGAAGCCAGACATGACAGATTTAGAAATTGTATATGGGAGGACA
AAACCCAGTTTTTCAATACAATGCCACCATCTTTAATTCCTTTGTCACCTGTTTCAGGTCAAAGAATGCAAATAATCAAT
GGTCTTCCTGTTACTAAAACAGCAATTTAAAAAACAGCTGCCCTTCAAGATGAGCTAACCTTTCTCCACTCCCAGATTGC
TGCAATTGTTGCATTGCAAGAGGCAGAAAACAAGTTAGTGTCGAGTCCTTGAAATCATATGATATACCTGGTATCTTGGG
CCCACTACCATCTGTGACTTCTTTACCCTCTCCTGTACCAGATTGTTCTTCAAATTCAGTGGTCCAC

Alignment

ORF - retro_mdom_1813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 54.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RQLLEYFGFPLEQFTPIWEAHANGRSIVRVIVTSLPSNLFSRTDLYQICSTILPSWENKEYGSTRSIVRS
          RQLLEY.GFP.EQFTPIWEAH.NGRSIVRVIVT.LPSNLFSRTDLYQICSTILPSWENKEYGST.SIV.S
Retrocopy RQLLEYLGFP*EQFTPIWEAHTNGRSIVRVIVTNLPSNLFSRTDLYQICSTILPSWENKEYGST*SIVHS

Parental  IGKILPLEPCPRPNFELFQYMKSLDCDQHGSALNPIVPSFADILCVANDEARQDRFRNCIWEKYEDKTQF
          IG.ILPLE.CPRPN.ELFQYMKSLD.DQHGSA..PIVP.FADILCV.NDEAR.DRFRNCIWE...DKTQF
Retrocopy IGNILPLEHCPRPNCELFQYMKSLDYDQHGSAQSPIVPLFADILCVPNDEARHDRFRNCIWE---DKTQF

Parental  FNPMPPPLIPLSPVSSQRMQIINGLPVTKAAIKKIAALQDELTILRSQIAAIVALQEAENKF-TLESLKS
          FN.MPP.LIPLSPVS.QRMQIINGLPVTK.AI.K.AALQDELT.L.SQIAAIVALQEAENK....ESLKS
Retrocopy FNTMPPSLIPLSPVSGQRMQIINGLPVTKTAI*KTAALQDELTFLHSQIAAIVALQEAENKL<SVESLKS

Parental  YDIPGNLGPLPSVTSSPSPVPDCSSNSVVH
          YDIPG.LGPLPSVTS.PSPVPDCSSNSVVH
Retrocopy YDIPGILGPLPSVTSLPSPVPDCSSNSVVH

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_1813 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1813 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
Canis familiaris	ENSCAFG00000000244	1 retrocopy	retro_cfam_1178,
Myotis lucifugus	ENSMLUG00000002331	1 retrocopy	retro_mluc_2227,
Monodelphis domestica	ENSMODG00000017453	1 retrocopy	retro_mdom_1813 ,
Nomascus leucogenys	ENSNLEG00000014793	1 retrocopy	retro_nleu_1513,
Pan troglodytes	ENSPTRG00000018634	1 retrocopy	retro_ptro_1491,