RetrogeneDB ID: retro_mdom_826

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:105758078..105758492(-)
• Located in intron of: ENSMODG00000000505

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACOT13
• Ensembl ID: ENSMODG00000025622
• Aliases: None
• Description: acyl-CoA thioesterase 13 [Source:HGNC Symbol;Acc:20999]

Sequence

>retro_mdom_826
CGGCTAGCGATGGGTGATAAGGCACTGAAGATTTTACAGGTACTGTTGAAGTCACGTGGCTTCGATGGCGTTTTACAAAA
GGTTACTCTTCTTTCTGCAAGTCCCGGAAAGGTGGTTTGTGAAATGAAAGTTGAAGAAGAGCATACTAATCTGCTGGGCA
CTCTACATGGTGGTTTAACAGCAACTCTGGTAGATGTTATATCTACGGTAGCTTTTCTCAACACAGAAAGGGGAGCACCT
GGAGTCAGTGTGGACATGAACATAACATACTTGTCCTCGGCTAAGCTAGGAGAAGAAATATTGATTGCTGCTCATGTTCT
GAAGCAAGGAAAAACTCTTGGCTTTGCAACTGTGGACCTGACAAACAAGATCACAGGAAAGTTGCTAGCGCAAGGCAGAC
ATACGAAACACCTA

Alignment

ORF - retro_mdom_826 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.51 %
• Parental protein coverage: 97.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLAMGPQTLQNLQQLLKAILDTRCFDRVLEKVTLLSASPGKVVCEMKVEEEHTNKLGTLHGGLTATLVDV
          RLAMG...L..LQ.LLK.....R.FD.VL.KVTLLSASPGKVVCEMKVEEEHTN.LGTLHGGLTATLVDV
Retrocopy RLAMGDKALKILQVLLKS----RGFDGVLQKVTLLSASPGKVVCEMKVEEEHTNLLGTLHGGLTATLVDV

Parental  ISTIAFINTERGAAGVSVDMNITYLSPAKLGEEILITAHVLKQGKTLGFASVDLTNKITGKLVAQGRHTK
          IST.AF.NTERGA.GVSVDMNITYLS.AKLGEEILI.AHVLKQGKTLGFA.VDLTNKITGKL.AQGRHTK
Retrocopy ISTVAFLNTERGAPGVSVDMNITYLSSAKLGEEILIAAHVLKQGKTLGFATVDLTNKITGKLLAQGRHTK

Parental  HL
          HL
Retrocopy HL

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_826 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_826 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025622	1 retrocopy	retro_mdom_826 ,