RetrogeneDB ID: retro_mdom_332

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:187810946..187811627(+)
• Located in intron of: ENSMODG00000001626

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACOT9
• Ensembl ID: ENSMODG00000007768
• Aliases: None
• Description: acyl-CoA thioesterase 9 [Source:HGNC Symbol;Acc:17152]

Sequence

>retro_mdom_332
AAGAGGTCAGGTTTTATAAATCAAATAGTCCTTAAAAGTCCAAAGGAAGGGGAACTCTTTAAGCTAACAGAATTGAATAA
GGGGAAGAAGACTGCCTTCCACATCCTTATTAAAGATGGCTCCAACTGCTGAAGAAAGAAATTCCATTTGTAACATGTTT
CTTAATACACTGGAGCTGAGGACTGTAAATTTTCAAAGTCAAGTTTTATCTCTGTATTCAAAGTGGATGGAAGATACAAA
ACTGAAGAGCCTTCACTAATGCCATCCTGAGAAAATGGAACATTTTCAATAGAGGTGTTGGAGATTTCCTTATGAGAAAA
GCATTTAAACTTGGTTTGGCTACAGCTTGTCAATTTGGTGGTTTTAGACCTTTACTAGCTGGTATAGATATTGCATTTAG
GAAACCCATTTCAAGTTGGATCACTACTATTTCTTTCTTCCCAGATTTATTTTACTGAGAATAATTACATTCAAATCAGA
TTGAATGTGACACTATCTTCACAGCAACACTAAAGTTCACAAGACTGGCAGTATCTTTCATTTCACATTTTTAGCAAAGA
AATGATATTGGTGATTCCCAAAACAAATGGAGAGTCTATGACGTTAGTAGATAATAAATGACATTTCATGTCCACAATGA
GAGGAACAAAGAATGAGTGGAAAAATTACTATTCAGTGTCT

Alignment

ORF - retro_mdom_332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 51.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KGPAFINPLVLETPEEEELFKQGELNKG-RRIALTTASLLKMAPTAEERNAIHDMFLNTLDSRTVTFESQ
          K...FIN..VL..P.E.ELFK..ELNKG.RR...T..SLLKMAPTAEERN.I..MFLNTL..RTV.F.SQ
Retrocopy KRSGFINQIVLKSPKEGELFKLTELNKG>RRLPST--SLLKMAPTAEERNSICNMFLNTLELRTVNFQSQ

Parental  VLRPDSKWMEDTILKSLHICHPEKR-NIFNRIFGGYLMRKAYELAWATAYQFCGSRAFLAAVDDIVFQSP
          VL...SKWMEDT.LKSLH.CHPEK..NIFNR..G..LMRKA..L..ATA.QF.G.R..LA..D.I.F..P
Retrocopy VLSLYSKWMEDTKLKSLH*CHPEKM>NIFNRGVGDFLMRKAFKLGLATACQFGGFRPLLAGID-IAFRKP

Parental  V-EIGSLLFLSSQVCYTEKNYIQVRVHSEVSLPY-TKEHKTTNIFHFTF-YAKENVPLVIPKTYGESMLF
          ....GSLLFLSSQ...TE.NYIQ.R.....S....TK.HKT..IFHFTF...KE...LVIPKT.GESM..
Retrocopy I>QVGSLLFLSSQIYFTENNYIQIRLNVTLSSQQ>TKVHKTGSIFHFTF<FSKEMI-LVIPKTNGESMTL

Parental  LDSRRHFRSVIEDTKDEWENSYPAS
          .D...HF.S....TK.EW.N.Y..S
Retrocopy VDNK*HFMSTMRGTKNEWKNYYSVS

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_332 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_332 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000007768	1 retrocopy	retro_mdom_332 ,
Mus musculus	ENSMUSG00000025287	1 retrocopy	retro_mmus_76,
Otolemur garnettii	ENSOGAG00000002305	1 retrocopy	retro_ogar_954,