RetrogeneDB ID: retro_mdom_1493

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:9421581..9422463(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACAT2
• Ensembl ID: ENSMODG00000007156
• Aliases: None
• Description: acetyl-CoA acetyltransferase 2 [Source:HGNC Symbol;Acc:94]

Sequence

>retro_mdom_1493
GCTCAGTCCATTGGATCTGGAGAGTCCAGTGTTGTCATAGCAGGAGGCATGGAGAGCATGATCAAGGTGCCTCATTTTGT
ACACTTAAAAACAGGATTGAAAATAGGTGAAACTCCCTTGAAGGACAGCGTGATCTGTGATGGGCTTACGGACGCATTCC
ACAACTACCACATGGGGATTACAGCTGAAAATGTGGCACAAAAATGGAAAGTGAGTAGAGAAGACCAAGATGGATATGCT
CTTTTGTCACAGAAGAGGAAGGAGAATGCTAAAATAGCAGGCTATTTTTACAAAGAGATTGTGCCTGTTTCTGTGCCTTC
TGGAAAAGGACCTGTGGAGGTGAAGACGGATGAATTTCCTCGCCATGGAAGCACTCTGGAGGCCATATCCAAACTCAAGT
CTTGCTTTCTGACAGATGGATCAGGAACAATAACTGCTGCCAATGCTTCAGGAATGGATGATGGAGCTGCTGCTGTGGTT
CTTATGAAGAAATCGGAAGCAGAAAGACAAGGTCTTACACCATTGGCACAGATTGTATCCTGGTCACAAGTTGGTGTAGA
CCCTTCCATTATGGGATCTAGACCAATTTCAGCCATCAGGCAGGCTGTTGCCAAAGCAAATTGGACACTAGATGATGTTG
ATGCATTTGAAATCAATGAAGCCTTTGCAACCCTGGCTGTAGCAGTATCAAAGGAGCTCAGATTGAATCCAGAAAAGGTC
AACATTCAAGGTGGAGCCATAACTTTGGGACATCCCATTGGGTCCTCAGGGTGTTGAATTCTTGTTACTCTGTTACATAC
ACTGGAGCAGATGGGTGGAACTCGTGGAGTGGCAGCTCTCTGCATTGGAGGAGGGATGGGAATAGCAATGTGTGTTAAAA
GA

Alignment

ORF - retro_mdom_1493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.54 %
• Parental protein coverage: 74.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AQSIGSGESSVVIAGGMESMSKAPHFVHLRTGLKMGETPLKDSVICDGLTDAFHNYHMGITAENVAQKWK
          AQSIGSGESSVVIAGGMESM.K.PHFVHL.TGLK.GETPLKDSVICDGLTDAFHNYHMGITAENVAQKWK
Retrocopy AQSIGSGESSVVIAGGMESMIKVPHFVHLKTGLKIGETPLKDSVICDGLTDAFHNYHMGITAENVAQKWK

Parental  VSREDQDGYALLSQKRTENAQKAGYFDKEIVPVSVPSRKGPVEVKTDEFPRHGSTLEAISKLKPCFLTDG
          VSREDQDGYALLSQKR.ENA..AGYF.KEIVPVSVPS.KGPVEVKTDEFPRHGSTLEAISKLK.CFLTDG
Retrocopy VSREDQDGYALLSQKRKENAKIAGYFYKEIVPVSVPSGKGPVEVKTDEFPRHGSTLEAISKLKSCFLTDG

Parental  SGTITAANASGMNDGAAAVVLMKKSEAERRGLTPLAQIVSWSQVGVDPSIMGSGPIPAIRQAVAKANWTL
          SGTITAANASGM.DGAAAVVLMKKSEAER.GLTPLAQIVSWSQVGVDPSIMGS.PI.AIRQAVAKANWTL
Retrocopy SGTITAANASGMDDGAAAVVLMKKSEAERQGLTPLAQIVSWSQVGVDPSIMGSRPISAIRQAVAKANWTL

Parental  DDVDAFEINEAFASLAVAVSKELGLNPEKVNIQGGAIALGHPIGSSGCRILVTLLHTLERMGGTRGVAAL
          DDVDAFEINEAFA.LAVAVSKEL.LNPEKVNIQGGAI.LGHPIGSSGC.ILVTLLHTLE.MGGTRGVAAL
Retrocopy DDVDAFEINEAFATLAVAVSKELRLNPEKVNIQGGAITLGHPIGSSGC*ILVTLLHTLEQMGGTRGVAAL

Parental  CIGGGMGIAMCVKR
          CIGGGMGIAMCVKR
Retrocopy CIGGGMGIAMCVKR

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_1493 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1493 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002827	1 retrocopy	retro_btau_560,
Callithrix jacchus	ENSCJAG00000011777	1 retrocopy	retro_cjac_1372,
Dasypus novemcinctus	ENSDNOG00000002502	1 retrocopy	retro_dnov_331,
Macaca mulatta	ENSMMUG00000012843	1 retrocopy	retro_mmul_277,
Monodelphis domestica	ENSMODG00000007156	1 retrocopy	retro_mdom_1493 ,
Rattus norvegicus	ENSRNOG00000019189	1 retrocopy	retro_rnor_1055,
Xenopus tropicalis	ENSXETG00000021174	1 retrocopy	retro_xtro_45,