RetrogeneDB ID: retro_mdom_1425

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:415308837..415309167(-)
• Located in intron of: ENSMODG00000018257

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_1425
AAGGTTCTCCTTCTGGATGAAGGCTTTCCCACATTCAGTACACTCAAAGGGTTTCTCTCCAGTATGAATTCTCTGATGTA
GAGTAAGATATGAGTTTTTACTGAAAGTTTTCCAACATTCAATGCATTCAAATGGCCTCTCTCTACTATGAGGTCTCTGA
TGTTCAGTAAAGATTGTCCTGTAGCAGAAGGCTTTCCCACATTGATTACATTCAAAGGGCTTCTCTCCAGCATGAATCCT
CTGATGTTCAATAAGGTTGCTCTTTTAACTGAAGATTTCCCCACACTGGTTACATTCAAATTGTTTCTGTCTAGCATGCA
TCATCTGATG

Alignment

ORF - retro_mdom_1425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.27 %
• Parental protein coverage: 92.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTYSLSESFPTFMTFKGFLSSMSSLMSIKVSLLTEGFSTFMAFKGFLTSMNSLMGNEVCPLSESFPTFMT
          K...L.E.FPTF.T.KGFLSSM.SLM..K....TE.F.TF.AFK..L..M.SLM....CP..E.FPT..T
Retrocopy KVLLLDEGFPTFSTLKGFLSSMNSLM*SKI*VFTESFPTFNAFKWPLSTMRSLMFSKDCPVAEGFPTLIT

Parental  FKGFLSSVSSLMGNKACLPAEAFPTFLTLKGFLSSMSSLM
          FKG.LSS...LM.NK..L..E.FPT..T.K.FLSSM..LM
Retrocopy FKGLLSSMNPLMFNKVALLTEDFPTLVTFKLFLSSMHHLM

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_1425 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1425 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.

---

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,