RetrogeneDB ID: retro_mdom_539

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:217742067..217742466(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000001911
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MLX
• Ensembl ID: ENSMODG00000014918
• Aliases: None
• Description: MLX, MAX dimerization protein [Source:HGNC Symbol;Acc:11645]

Sequence

>retro_mdom_539
CTGCAGGTGGAATACACCTACAGTGACAACAGCCTGGACCCGCCGTATTTTGTAGAAAGTAACCGAAAAGGGATTGTAGT
GTCCAGAACCAACAGCATCGACTTCACCAGTGCTTCCTCAGTTTCCAACACAGATGATGACGACAGTGATTACCAGCAAG
AATCCTACAAAGAATCATATAAGGAGAGGAGGCGCTGGGCCCACACACAAGCAGAACAGAAGAGGAGAGATGCCATCAAG
AGAGGCCACGAAGATCTTCAAGCCACAATCCCCACCTGTCAGCAGCAAGATTGCTCCATTGGCTCCCAGAAACTCAGCAA
GGCCATTGTTCTGCAGAAGACCATTGATTATATCCAGTTCTTGCATAAAGAGGAGAAACAGGAGGAGGAAGTCTCTACC

Alignment

ORF - retro_mdom_539 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.07 %
• Parental protein coverage: 54.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKVEYTYSDNSLDPGLFVESNRKGSVVSRANSIGSTSASSVPNTDDEDSDYQQEPYKESYKDRRRRAHTQ
          ..VEYTYSDNSLDP..FVESNRKG.VVSR.NSI..TSASSV.NTDD.DSDYQQE.YKESYK.RRR.AHTQ
Retrocopy LQVEYTYSDNSLDPPYFVESNRKGIVVSRTNSIDFTSASSVSNTDDDDSDYQQESYKESYKERRRWAHTQ

Parental  AEQKRRDAIKRGYDDLQAIVPTCQQQDFSIGSQKLSKAIVLQKTIDYIQFLHKEKKKQEEEVST
          AEQKRRDAIKRG..DLQA..PTCQQQD.SIGSQKLSKAIVLQKTIDYIQFLHKE..KQEEEVST
Retrocopy AEQKRRDAIKRGHEDLQATIPTCQQQDCSIGSQKLSKAIVLQKTIDYIQFLHKE-EKQEEEVST

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	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_539 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_539 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005011	1 retrocopy	retro_cjac_2774,
Homo sapiens	ENSG00000108788	1 retrocopy	retro_hsap_2216,
Gorilla gorilla	ENSGGOG00000010869	1 retrocopy	retro_ggor_1748,
Microcebus murinus	ENSMICG00000010258	1 retrocopy	retro_mmur_1373,
Monodelphis domestica	ENSMODG00000014918	2 retrocopies	retro_mdom_501, retro_mdom_539 ,
Nomascus leucogenys	ENSNLEG00000011638	1 retrocopy	retro_nleu_2338,
Pongo abelii	ENSPPYG00000008387	1 retrocopy	retro_pabe_2087,
Pan troglodytes	ENSPTRG00000009208	1 retrocopy	retro_ptro_1681,