RetrogeneDB ID: retro_mdom_1350

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:104032559..104032919(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000003226
• Aliases: None
• Description: None

Sequence

>retro_mdom_1350
AAGATCTTAGATTTGGGGATTGTAGACCTCAACCCTGAGAGTTTCAAGATCAGTTTGGCATGTAGGGACTCCGAACACCC
TCCTGTCGATGTGGCCATAGAACTGAAAGCTTTATTTACAGATAGCCAACTGATTAGAAATTCTTGTATATCTGGAGAAA
GAGGTGAAGAACAATCAGCAATTCCTTATTTTCCGTTTATTCCAGATCAGCCTTTTAAGGGGGAAATTCTCTGTGAACAC
TCATAAGTTAGAGTATTTGTGGATGGACACCAGCTTTTTTATTTTTACTATTGAATTGAAACACTGCCTGAAATTGACAC
AATAAAGGTCAATGGAGACCTCCAGATCATTCAACTTGGC

Alignment

ORF - retro_mdom_1350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 69.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KILVMGIVDLNPESFKISLTCGDSEDPPADVAIELKAVFTDKQLIRNSCISGERGEEQSAIPYFPFIPDQ
          KIL..GIVDLNPESFKISL.C.DSE.PP.DVAIELKA.FTD.QLIRNSCISGERGEEQSAIPYFPFIPDQ
Retrocopy KILDLGIVDLNPESFKISLACRDSEHPPVDVAIELKALFTDSQLIRNSCISGERGEEQSAIPYFPFIPDQ

Parental  PFRVEILCEHPRFRVFVDGHQLFDFYHRIETLSAIDTIKINGDLQITKLG
          PF..EILCEH...RVFVDGHQLF.FY..IETL..IDTIK.NGDLQI..LG
Retrocopy PFKGEILCEHS*VRVFVDGHQLFYFYY*IETLPEIDTIKVNGDLQIIQLG

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	35.76 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	31.63 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1350 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1350 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001067	1 retrocopy	retro_amel_429,
Bos taurus	ENSBTAG00000000156	1 retrocopy	retro_btau_1263,
Dasypus novemcinctus	ENSDNOG00000015222	1 retrocopy	retro_dnov_493,
Felis catus	ENSFCAG00000001209	1 retrocopy	retro_fcat_1280,
Monodelphis domestica	ENSMODG00000003226	2 retrocopies	retro_mdom_1350 , retro_mdom_233,
Mus musculus	ENSMUSG00000042363	3 retrocopies	retro_mmus_1637, retro_mmus_272, retro_mmus_2942,
Sarcophilus harrisii	ENSSHAG00000011885	2 retrocopies	retro_shar_315, retro_shar_732,