RetrogeneDB ID: retro_mdom_509

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:94414302..94414656(-)
• Located in intron of: ENSMODG00000028448

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTD1
• Ensembl ID: ENSMODG00000005696
• Aliases: None
• Description: D-tyrosyl-tRNA deacylase 1 [Source:HGNC Symbol;Acc:16219]

Sequence

>retro_mdom_509
ATGAAGGCTATCGTCCATCCCGTCTTGCAGGCCAGCATCACAGTTGGAGAGGAGCAGATAAGTTCCATTGGACGGGGCAT
TTGTGTGTTGCTGGGTATTTCTATGAAAGATACACAGAAAGACCTGGAAAACATGGTTCAAAAGATTTTAAATCTGTGGG
TATTTGAAGATTAAAGTGGAAAATGCTGGTCAAAAAGTGTGATGGACCAACAGTATGAAGTGTTGTGTGTTAGCCAGTAT
ATTCTTCAATGTATTTTAAAAGAGAACAAACCAGACTATCATATGGCCATGTCTATGGAGCAATAGGATACCTTCTACAA
GAACTTCCTTGAACCAATGAGAAAAGCTTATAAA

Alignment

ORF - retro_mdom_509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKAIIQRVTRASVTVGEEQISSIGRGICVLLGISMEDTQKELEHMVRKILNLRVFEDESGKHWSKSVMDK
          MKAI...V..AS.TVGEEQISSIGRGICVLLGISM.DTQK.LE.MV.KILNL.VFED.SGK.WSKSVMD.
Retrocopy MKAIVHPVLQASITVGEEQISSIGRGICVLLGISMKDTQKDLENMVQKILNLWVFED*SGKCWSKSVMDQ

Parental  QYEVLCVSQFTLQCILKGNKPDYHMAMPTEQAETFYKNFLEQLRKAYK
          QYEVLCVSQ..LQCILK.NKPDYHMAM..EQ..TFYKNFLE..RKAYK
Retrocopy QYEVLCVSQYILQCILKENKPDYHMAMSMEQ*DTFYKNFLEPMRKAYK

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	32.54 RPM
SRP007412_cerebellum	0.00 RPM	43.74 RPM
SRP007412_heart	0.00 RPM	62.60 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	6.04 RPM
SRP007412_testis	0.00 RPM	36.54 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_509 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_509 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008964	1 retrocopy	retro_btau_767,
Macropus eugenii	ENSMEUG00000009170	2 retrocopies	retro_meug_137, retro_meug_1809,
Macaca mulatta	ENSMMUG00000012880	1 retrocopy	retro_mmul_217,
Monodelphis domestica	ENSMODG00000005696	1 retrocopy	retro_mdom_509 ,
Mus musculus	ENSMUSG00000027430	1 retrocopy	retro_mmus_2774,
Oryctolagus cuniculus	ENSOCUG00000010988	1 retrocopy	retro_ocun_1357,
Tupaia belangeri	ENSTBEG00000000242	1 retrocopy	retro_tbel_3434,