RetrogeneDB ID: retro_mdom_1564

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:293881582..293882344(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP3M1
• Ensembl ID: ENSMODG00000000660
• Aliases: None
• Description: adaptor-related protein complex 3, mu 1 subunit [Source:HGNC Symbol;Acc:569]

Sequence

>retro_mdom_1564
GGCAATAGTAATGTTGGAGACACACTCCCCACTGGTCAGCTTTCCAACATCCCATGGTGTCGTGCAGGTGTGAAATATAT
AAACAATGAAGCTTATTTTGATGTCATTGAAGAAATAGATGCAATTATAGACAAATCAGCTTCCACAGTCTTTGCAGAAA
TTCAAGGTGTCATTGATGCTTGCATTAAGCTTTCCGGAATGCTTGATCTTTCCCTTTCTTTCATGAACCCAAGGCTTCCA
GATGATGTCAGCTTCCGCCCCTGCATTCGTTTCAAACGCTGGGAGGCAGAAAGAGTCCCGTCATTTATTCCTCCAGATGG
AAACTTCCGACTCATTTCCTACCATGTCAGCTCACAAAATTTAGTGGCAGTTCCAGTGTATGTGAAACAAAGCATCAGCT
TTAAGGAGAACAGCTCTTGTGGCAGATACGATATTACAATTGGACCAAAGCAAAGCATGGGAAAAACAACTGAAGGAATC
ACAGGGACTGTTCACATGCCCAACGTTGTATTGAATATGAACCTAACTCCAACACAAGGCAGCTACACGTGTGATCCAGT
CACCAAGGTCTTAACGTGGGACGTTGGGAAAATTACCCCCCACATGCTCCCAAGTCTTAAAGGATTGGTGAATTTATAGT
CTGGAGCCCCCAAACCTGAAGAAAGCCCAAGCCTCAACATTCAGCAACTTGCTATTTCAGGCTTGAAAGTCAATCGCCTT
GATATGTATGGAGAGAAATATAAGCCATTTAAAGGAGTCAAA

Alignment

ORF - retro_mdom_1564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.92 %
• Parental protein coverage: 61.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVIEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDL
          G.SNVGDTLPTGQLSNIPW.RAGVKY.NNEAYFDVIEEIDAIIDKS.STVFAEIQGVIDACIKLSGM.DL
Retrocopy GNSNVGDTLPTGQLSNIPWCRAGVKYINNEAYFDVIEEIDAIIDKSASTVFAEIQGVIDACIKLSGMLDL

Parental  SLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSISFKENSSC
          SLSFMNPRL.DDVSF.PCIRFKRWE.ERV.SFIPPDGNFRLISY.VSSQNLVA.PVYVK.SISFKENSSC
Retrocopy SLSFMNPRLPDDVSFRPCIRFKRWEAERVPSFIPPDGNFRLISYHVSSQNLVAVPVYVKQSISFKENSSC

Parental  GRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLTWDVGKITPQKLPSLKGLV
          GR.DITIGPKQ.MGKT.EGIT.TVHMP.VVLNMNLTPTQGSYT.DPVTKVLTWDVGKITP..LPSLKGLV
Retrocopy GRYDITIGPKQSMGKTTEGITGTVHMPNVVLNMNLTPTQGSYTCDPVTKVLTWDVGKITPHMLPSLKGLV

Parental  NLQSGAPKPEENPSLNIQFKIQQLAISGLKVNRLDMYGEKYKPFKGVK
          NL.SGAPKPEE.PSLNIQ....QLAISGLKVNRLDMYGEKYKPFKGVK
Retrocopy NL*SGAPKPEESPSLNIQ----QLAISGLKVNRLDMYGEKYKPFKGVK

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	123.85 RPM
SRP007412_cerebellum	0.00 RPM	181.51 RPM
SRP007412_heart	0.00 RPM	122.80 RPM
SRP007412_kidney	0.00 RPM	330.52 RPM
SRP007412_liver	0.00 RPM	172.70 RPM
SRP007412_testis	0.00 RPM	157.74 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1564 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1564 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004510	1 retrocopy	retro_chof_2586,
Monodelphis domestica	ENSMODG00000000660	1 retrocopy	retro_mdom_1564 ,
Monodelphis domestica	ENSMODG00000005838	2 retrocopies	retro_mdom_1571, retro_mdom_451,
Mus musculus	ENSMUSG00000021824	1 retrocopy	retro_mmus_580,
Ictidomys tridecemlineatus	ENSSTOG00000012881	1 retrocopy	retro_itri_1276,