RetrogeneDB ID: retro_mdom_1972

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:15021058..15021405(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000023141
• Aliases: None
• Description: None

Sequence

>retro_mdom_1972
TCTCTGATGTTTTAAAAGGTGTTGTCTTACACTGAAAGTTTTTCCATATTTGTTACATTCAAATAGTTTCTCTCCAGTAT
GAGTACTCTGATGAATAGTAAGATGTCCCTTTTGATTAAAAGCTTTCCCACATTCATTACATTCAAATGGTTTCTCTCCA
GTATGAGTCATTTGATGCCTGACAAGTAATTTTTTACCCTGAAAATTTTCCCACATTCTTTACATTGAAATGGTTTCTCT
CCAGTGTGAATTCCCTGATGGCAAATAAGATGATCTTTCCTGTTAAAAGCTTTCCCATATTCATTACATTCACATTGTTT
CTTCTTAGTATGAGTTCTCTGATGGGT

Alignment

ORF - retro_mdom_1972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.26 %
• Parental protein coverage: 97.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLMDNKTYSLSESFPTFMTFKGFLSSMSSLMSIKVSLLTEGFSTFMAFKGFLTSMNSLMGN-EVCPLSES
          SLM..K..S..ESF..F.TFK.FLSSMS.LM..K.SLL...F.TF..FK.FL.SM..LM....V....E.
Retrocopy SLMF*KVLSYTESFSIFVTFK*FLSSMSTLMNSKMSLLIKSFPTFITFKWFLSSMSHLMPD<QVIFYPEN

Parental  FPTFMTFKGFLSSVSSLMGNKACLPAEAFPTFLTLKGFLSSMSSLMG
          FPTF.T.K.FLSSV.SLM.NK...P...FP.F.T...FL.SMSSLMG
Retrocopy FPTFFTLKWFLSSVNSLMANKMIFPVKSFPIFITFTLFLLSMSSLMG

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_1972 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1972 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007018	1 retrocopy	retro_dnov_33,
Monodelphis domestica	ENSMODG00000023141	4 retrocopies	retro_mdom_1425, retro_mdom_1832, retro_mdom_1972 , retro_mdom_797,
Monodelphis domestica	ENSMODG00000023689	1 retrocopy	retro_mdom_1214,