RetrogeneDB ID: retro_mdom_160

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:250364668..250365121(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023568
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005746
• Aliases: None
• Description: None

Sequence

>retro_mdom_160
GACTTTGAATCCTATTTGAGAAATATAAAATCACAATATGAAGTTTTTCGAAGTAGTAGGCTTTCATCAGAGGCTACAGT
TTTGACACCAAACACAGAAAGTAGTTGTGACTTAATGACCAAAACAAAATCAACAAGTGGAAATGATGACAGCACGTCCC
TAGATCTAGAATGGGAAGATGAAGAAGGAGTGAATAGAATGGTCCCTTTGAGAGAACGTTCCAAAACGGAAGAGGATATT
CTTCAAGCTGCATTAAAATATAGCAGTAAGAAGACGGGAAGTAACCCTACCTCAGCTTCTGATGATTCTAATGGGCTGGA
GTGGGAGAATGATTTTGTTAGTGCTGAAATGGATAACAATGGCAATTCCGAATATTCTGGATTTGTGAATCCTGTTTTAG
AACTGTCTGCCTCTGAGTTAAAGACCTTGGAAGCAGATCAGCAGGACAGATAG

Alignment

ORF - retro_mdom_160 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.67 %
• Parental protein coverage: 57.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFESYLRNIKSQYEVFRSSRLSSEATVLTPNTESSCDLMTKTKSTSGNDDSTSLDLEWEDEEGMNRMVPL
          DFESYLRNIKSQYEVFRSSRLSSEATVLTPNTESSCDLMTKTKSTSGNDDSTSLDLEWEDEEG.NRMVPL
Retrocopy DFESYLRNIKSQYEVFRSSRLSSEATVLTPNTESSCDLMTKTKSTSGNDDSTSLDLEWEDEEGVNRMVPL

Parental  RERSKTEEDILRAALKYSSKKTGSNPTSASDDSNGLEWENDFVSAEMDNNGNSEYSGFVNPVLELSASEL
          RERSKTEEDIL.AALKYSSKKTGSNPTSASDDSNGLEWENDFVSAEMDNNGNSEYSGFVNPVLELSASEL
Retrocopy RERSKTEEDILQAALKYSSKKTGSNPTSASDDSNGLEWENDFVSAEMDNNGNSEYSGFVNPVLELSASEL

Parental  KTLEADQQDR
          KTLEADQQDR
Retrocopy KTLEADQQDR

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_160 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_160 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007262	2 retrocopies	retro_chof_1995, retro_chof_8,
Monodelphis domestica	ENSMODG00000005746	1 retrocopy	retro_mdom_160 ,
Oryctolagus cuniculus	ENSOCUG00000004413	1 retrocopy	retro_ocun_91,
Otolemur garnettii	ENSOGAG00000001631	1 retrocopy	retro_ogar_1054,
Sus scrofa	ENSSSCG00000009128	1 retrocopy	retro_sscr_245,