RetrogeneDB ID: retro_mdom_314

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:94644610..94645170(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCHY1
• Ensembl ID: ENSMODG00000019197
• Aliases: None
• Description: ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:17479]

Sequence

>retro_mdom_314
CAAATCTGTGAAGAATGTAGCACTGTATTTGAAGTATGTTATTGCAATATATGCCAGTATTTGACAAAGATGAGAACCAA
CACCAATGCGGGAAGTGTGAAATTTGTAGGGCTTTTCCAAAGGAACACATTTTTCACCCTTTAAAATGTAACTTAAGCCT
AACCTTTTCTCTCTAAGGATACCATAAATGCACTGAGAATGTCTCTAGGCAGAGTTGTTCCACATGTTTAGAGGACATTC
ACACAGACTGGGTAGTTGTTCATGTCTTGCCATGTGTATATCTTCTACCTAGAATATGTTGTGAAAAAATATTAAAAGGA
GGCTACAGATGTCCATTATGTAAGCACTCTACTCTAGATATAACTCACTATTGGCAACAGTTAAATAATAGAGTTCTACA
AAGTCCAATGGCAACAGAATATCAGAATATGACTATGGAAATTTTCTGCAATGATTGCTGGGTTCACTCTACAGTTCAGA
TCTACATGTTAGGAATGGAATGCAAGCATTGAATAAATACTGCCCAACACTGAGGATATGGAATTTCTTTAGAACAAAAG

Alignment

ORF - retro_mdom_314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.26 %
• Parental protein coverage: 79.41 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QICEECSTVFGEYYCNICH-LFDKDKKQYHCEKCGICRIGPKEDFFHCLKCNLCLSLSLQGHHKCIENVS
          QICEECSTVF...YCNIC...FDKD..Q..C.KC.ICR..PKE..FH.LKCNL.L..SL.G.HKC.ENVS
Retrocopy QICEECSTVFEVCYCNICQ<VFDKDENQHQCGKCEICRAFPKEHIFHPLKCNLSLTFSL*GYHKCTENVS

Parental  RQNCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCMHSALDMTRYWRQLDNEVAQTPMPT
          RQ.C..CLEDIHT..VV.HVLPC..LL.R.C.E..LK.GYRCPLC.HS.LD.T.YW.QL.N.V.Q.PM.T
Retrocopy RQSCSTCLEDIHTDWVVVHVLPCVYLLPRICCEKILKGGYRCPLCKHSTLDITHYWQQLNNRVLQSPMAT

Parental  EYQNMTVEILCNDCSARSTVQFHILGMKCKSCESYNTAQDGGCGIPLEQQ
          EYQNMT.EI.CNDC...STVQ...LGM.CK.....NTAQ..G.GI.LEQ.
Retrocopy EYQNMTMEIFCNDCWVHSTVQIYMLGMECK--H*INTAQH*GYGISLEQK

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	0.00 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_314 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_314 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032536	1 retrocopy	retro_cfam_1449,
Choloepus hoffmanni	ENSCHOG00000011650	1 retrocopy	retro_chof_1142,
Macropus eugenii	ENSMEUG00000003266	1 retrocopy	retro_meug_1564,
Monodelphis domestica	ENSMODG00000019197	2 retrocopies	retro_mdom_314 , retro_mdom_991,
Rattus norvegicus	ENSRNOG00000002546	2 retrocopies	retro_rnor_1127, retro_rnor_607,
Tursiops truncatus	ENSTTRG00000013786	1 retrocopy	retro_ttru_1333,