RetrogeneDB ID: retro_mdom_1256

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:121556364..121556550(+)
• Located in intron of: ENSMODG00000000380

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP1LC3A
• Ensembl ID: ENSMODG00000002694
• Aliases: None
• Description: microtubule-associated protein 1 light chain 3 alpha [Source:HGNC Symbol;Acc:6838]

Sequence

>retro_mdom_1256
AAAGAAGTGAGGCACATTTGAGAGAAGCTTCCCACCAAGACACCGGTGATAAAAGAAAGATAAAGGGCCAAGAAATAACT
TTCTGTACTGGATAAAGCCACATTCCTTGTACCAGATCATGTCAACCTGAGTGAGCTAATCAAAATAATTAGAAGGTGCC
TACAGCCAAATGTTACCCAAGCTTTC

Alignment

ORF - retro_mdom_1256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.13 %
• Parental protein coverage: 51.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEVQQIREQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAF
          KEV..I.E..P.K.PVI.ER....K.L.VLDK..FLVPDHVN.SEL.KIIRR.LQ.N.TQAF
Retrocopy KEVRHI*EKLPTKTPVIKER*RAKK*LSVLDKATFLVPDHVNLSELIKIIRRCLQPNVTQAF

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	228.14 RPM
SRP007412_cerebellum	0.00 RPM	469.12 RPM
SRP007412_heart	0.00 RPM	500.17 RPM
SRP007412_kidney	0.00 RPM	255.47 RPM
SRP007412_liver	0.00 RPM	306.62 RPM
SRP007412_testis	0.00 RPM	84.07 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1256 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1256 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
Echinops telfairi	ENSETEG00000012407	1 retrocopy	retro_etel_1766,
Felis catus	ENSFCAG00000022040	1 retrocopy	retro_fcat_1634,
Monodelphis domestica	ENSMODG00000002694	1 retrocopy	retro_mdom_1256 ,
Mustela putorius furo	ENSMPUG00000017814	1 retrocopy	retro_mputfur_1049,
Ictidomys tridecemlineatus	ENSSTOG00000006158	2 retrocopies	retro_itri_287, retro_itri_988,