RetrogeneDB ID: retro_mdom_721

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:229589275..229589641(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM1
• Ensembl ID: ENSMODG00000007076
• Aliases: None
• Description: LYR motif containing 1 [Source:HGNC Symbol;Acc:25074]

Sequence

>retro_mdom_721
ATGACAATGGCAACACGACAAGAAATTCTTGGCCTGTACCGCAAGATTTTCAGGCTTGCAAGGAGGTGGCATGAAGCATC
AGGGCAGACGGAAGACACCATCAGAGAAAAGCAGTATATTATAAATAAAGCCAGAATGTTGTTCCAGAAAAACAAAAATC
TTACAGATTCAGAACTGATTAAACAATGTATAGATGAATGCACAGTGAGAATTGAAATAGGATTGCTTTATCAGATCCCA
TATCCAAGGCCGATTCACCTGCCTCCAACTGCCCTCTCTCCCCTTCAAAGTTGTGAATTTCAAAACCAGGAGAAGCTAAG
GAAACTTTCCAGACCATTATATTTCAAGTCTCATGTTGAAATTTTG

Alignment

ORF - retro_mdom_721 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.16 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTATRQEVLGLYRKIFRLARRWHAASGQMEDTIREKQYIINEARILFQKNKNLTDSELIKQCIDECTAR
          MT.ATRQE.LGLYRKIFRLARRWH.ASGQ.EDTIREKQYIIN.AR.LFQKNKNLTDSELIKQCIDECT.R
Retrocopy MTMATRQEILGLYRKIFRLARRWHEASGQTEDTIREKQYIINKARMLFQKNKNLTDSELIKQCIDECTVR

Parental  IEIGLHYQIPYPRPIHLPPTALSPLQSRGFQNQEKLRKLSRPLYLKSHDEIL
          IEIGL.YQIPYPRPIHLPPTALSPLQS..FQNQEKLRKLSRPLY.KSH.EIL
Retrocopy IEIGLLYQIPYPRPIHLPPTALSPLQSCEFQNQEKLRKLSRPLYFKSHVEIL

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_721 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_721 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008951	1 retrocopy	retro_cpor_873,
Monodelphis domestica	ENSMODG00000007076	3 retrocopies	retro_mdom_1844, retro_mdom_721 , retro_mdom_807,
Sarcophilus harrisii	ENSSHAG00000006127	6 retrocopies	retro_shar_156, retro_shar_270, retro_shar_709, retro_shar_795, retro_shar_798, retro_shar_801,