RetrogeneDB ID: retro_mdom_303

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:48203781..48204335(+)
• Located in intron of: ENSMODG00000016112

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABHD5
• Ensembl ID: ENSMODG00000015241
• Aliases: None
• Description: abhydrolase domain containing 5 [Source:HGNC Symbol;Acc:21396]

Sequence

>retro_mdom_303
AGGATGAAGCACATTATCTTAGTGGAGCTGTAGGGTTTTCTAGAGAGACCTGATAGTATTGATCAAGACAGGCCAATTTC
AGTGTGGATCAAAGCCTTGGGAGCTGTACTGACCCCTTTAATCCCTTAGCTGGCCTTAGAATTGCAGGACCCTTTGGCTT
AAGCCTTGTGCAATGTTTAAAGCCCAATTTTAAGAGAAAATATGTTTCAATATTTGAAGATGATATTATGACAGACTATA
TCTACCACTGTAATGTAATGTAATATAAACAGACACCCAGTGGTGAAACTGCCTTTAGAAATATGACTATTTCTTATGGA
TGGGCCAAAAGACCAATGATCATGCGGATTGGGAAGATGGATCCAGACATTCTGATTTCTGTCATCTATGGAGCCCGATC
TTGCCTAGATGGCCATTCTGGCAACACCATCTAGTCCCTAAGGCCACATTCATATGTGAAGACTATTGCTATCCTTGGCA
CCAGACATTATGGCTACGCTGACCACCCAGAAGAATTCAACCAAAAAGCAAAGGAGATTTGTGATTCTGTGGAC

Alignment

ORF - retro_mdom_303 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 52.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RVKHLILVEPWGFPERPDSADQDRPIPVWIKALGAVLTP-FNPLAGLRIAGPFGLSLVQRLRPDFKRKYA
          R.KH.ILVE..GF.ERPDS.DQDRPI.VWIKALGAVLTP.FNPLAGLRIAGPFGLSLVQ.L.P.FKRKY.
Retrocopy RMKHIILVEL*GFLERPDSIDQDRPISVWIKALGAVLTP<FNPLAGLRIAGPFGLSLVQCLKPNFKRKYV

Parental  SMFEDDTVTEYIYHCNV----QTPSGETAFRNMTIPYGWAKRPMIMRIGKMDPDIPISVIYGARSCIDGN
          S.FEDD..T.YIYHCNV....QTPSGETAFRNMTI.YGWAKRPMIMRIGKMDPDI.ISVIYGARSC.DG.
Retrocopy SIFEDDIMTDYIYHCNVM*YKQTPSGETAFRNMTISYGWAKRPMIMRIGKMDPDILISVIYGARSCLDGH

Parental  SGHTIQSLRPHSYVKTIAILGAGHYVYADQPEEFNQKVKEICDSVD
          SG.TI.SLRPHSYVKTIAILG..HY.YAD.PEEFNQK.KEICDSVD
Retrocopy SGNTI*SLRPHSYVKTIAILGTRHYGYADHPEEFNQKAKEICDSVD

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	0.12 RPM	0.00 RPM
SRP007412_cerebellum	0.65 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	1.32 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	0.39 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_303 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_303 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
Echinops telfairi	ENSETEG00000012926	1 retrocopy	retro_etel_2204,
Monodelphis domestica	ENSMODG00000015241	1 retrocopy	retro_mdom_303 ,
Mustela putorius furo	ENSMPUG00000012931	1 retrocopy	retro_mputfur_1264,