RetrogeneDB ID: retro_mdom_1285

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:291540268..291540943(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENDOU
• Ensembl ID: ENSMODG00000009733
• Aliases: None
• Description: endonuclease, polyU-specific [Source:HGNC Symbol;Acc:14369]

Sequence

>retro_mdom_1285
CTCTACAGCTATGTAAATGAAGACCTTTTCTCCAAACCAACCTATGGTGCATTCATCAGTCTACTCAATAACTACCACCA
GGTAACAGGTCAGGGGGAACACTTCAGTTCTCAGCAGCTTGAAGAACAAGACGCTTTTCTTCAAGAGATAATGAAGACAG
CGGTCATGAAGGAACTCTATGGCTTCCTCCATCAAAAAAACAGATACAGCTCAGAGCAATAATTTGTCAGTGACCTGAAG
AAGCTGTGGTTTGGGTTGTATTCCTGGGGCCATGATGAAGGTGACTCCAGTGGCTTTAAACATGTTTTCTCCAGTGAAGT
GAAAAAGGGAAAAGTGTCAGGATTCCATAACTGGATCTGCTTCTACTTGCAGGAGAAGGAGGGTCTGGTCAACTATTATA
GCCATAACTATGATGGGCTTTGAGACTCATATTCTGATGTTCTAGGAAGGTAATTCAACTGGGATGGCTACTTCAAAGAA
GTGGGATTGGCCTTCATTGGCAGTAGTCTGGAGTTTGCTTTCTATTCCTTGTGCTTCATCAGCTGGCCTGGTGGTGTGGG
TCATTTGAGCCTAGGTGGGTACCCCCTGGCTATCCAAGCCTATACCTGGGACAAGGTGACCTATGGAAATGGCAAGAAGT
ACATTGCTACAGCCTTTATAGTATCTTCTATGAAT

Alignment

ORF - retro_mdom_1285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.67 %
• Parental protein coverage: 55.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYSYVNEELFSKPTYAAFISLLNNYHRVTGQGEHFSSQQLEEQDTFLREIMKTAVMKELYGFLHQKNRYS
          LYSYVNE.LFSKPTY.AFISLLNNYH.VTGQGEHFSSQQLEEQD.FL.EIMKTAVMKELYGFLHQKNRYS
Retrocopy LYSYVNEDLFSKPTYGAFISLLNNYHQVTGQGEHFSSQQLEEQDAFLQEIMKTAVMKELYGFLHQKNRYS

Parental  SEQEFVSDLKKMWFGLYSRGHDEGDSSGFEHVFSGEVKKGKVSGFHNWIRFYLQEKEGLVDYYSHNYDGP
          SEQ.FVSDLKK.WFGLYS.GHDEGDSSGF.HVFS.EVKKGKVSGFHNWI.FYLQEKEGLV.YYSHNYDG.
Retrocopy SEQ*FVSDLKKLWFGLYSWGHDEGDSSGFKHVFSSEVKKGKVSGFHNWICFYLQEKEGLVNYYSHNYDGL

Parental  WDSYPDVLGMQFNWDGYFKEVGSAFIGSSPEFEFALYSLCFISRPGGVCHLSLGGYPLAIKTYTWDKVTY
          .DSY.DVLG..FNWDGYFKEVG.AFIGSS...EFA.YSLCFIS.PGGV.HLSLGGYPLAI..YTWDKVTY
Retrocopy *DSYSDVLGR*FNWDGYFKEVGLAFIGSS--LEFAFYSLCFISWPGGVGHLSLGGYPLAIQAYTWDKVTY

Parental  GNGKKYIATAYIVSSTN
          GNGKKYIATA.IVSS.N
Retrocopy GNGKKYIATAFIVSSMN

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_1285 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1285 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009733	2 retrocopies	retro_mdom_1285 , retro_mdom_962,