RetrogeneDB ID: retro_mdom_561

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:307326975..307327404(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLOC1S6
• Ensembl ID: ENSMODG00000017628
• Aliases: None
• Description: biogenesis of lysosomal organelles complex-1, subunit 6, pallidin [Source:HGNC Symbol;Acc:8549]

Sequence

>retro_mdom_561
TCTGGCGATGCTTCTCCAGATGAAGGGCTAATGGAAGACTTGACAGTTGAAAATAAAGCTCTGGAACAACTAGCACAAGG
ATTACTCTCTCATTATTTACCAGATTTGGAGAGATCAAAGCAAGCCCTCCAGGAACTCACACAGAACCACGTGGTACTAC
TAGATACACTAGAGCAAGAGATTTCAAAATTCAACGAATGCCATTCTATTTTGGATATTAATACTTTGTTTACAGAAGCT
AAATTCTATCACAACAAGTTAGTGAATATTAGAAAAGAGATGCTGATACTTCATGAAAAGACCCCAAAATTTAAAAAAAG
ATCTCTAAAGCTCCAACAGAAGAGACAGAAAGAAGAATTGGAGTGGGAACAACAACAAGAAAAAGAATTTAAAAGAGAGA
AATAATTAACTACTAAACCAGCAAAAAGG

Alignment

ORF - retro_mdom_561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.61 %
• Parental protein coverage: 81.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGDASPDEGLMEDLTVENKALEQLAQGLLSHYLPDLERSKQALQELTQNQVVLLDTLEQEISKFKECHSI
          SGDASPDEGLMEDLTVENKALEQLAQGLLSHYLPDLERSKQALQELTQN.VVLLDTLEQEISKF.ECHSI
Retrocopy SGDASPDEGLMEDLTVENKALEQLAQGLLSHYLPDLERSKQALQELTQNHVVLLDTLEQEISKFNECHSI

Parental  LDINALFTEAKFYHNKLVNIRKEMLMLHEKTSKLKKRALKLQQKRQKEELEREQQREKEFEREKQLTAKP
          LDIN.LFTEAKFYHNKLVNIRKEML.LHEKT.K.KKR.LKLQQKRQKEELE.EQQ.EKEF.REK.LT.KP
Retrocopy LDINTLFTEAKFYHNKLVNIRKEMLILHEKTPKFKKRSLKLQQKRQKEELEWEQQQEKEFKREK*LTTKP

Parental  AKR
          AKR
Retrocopy AKR

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	9.77 RPM
SRP007412_cerebellum	0.00 RPM	5.88 RPM
SRP007412_heart	0.00 RPM	10.77 RPM
SRP007412_kidney	0.00 RPM	9.22 RPM
SRP007412_liver	0.00 RPM	6.04 RPM
SRP007412_testis	0.00 RPM	9.63 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_561 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_561 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 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012059	7 retrocopies	retro_chof_1342, retro_chof_20, retro_chof_2054, retro_chof_2102, retro_chof_211, retro_chof_248, retro_chof_600,
Dasypus novemcinctus	ENSDNOG00000019785	5 retrocopies	retro_dnov_1687, retro_dnov_1885, retro_dnov_2009, retro_dnov_2411, retro_dnov_275,
Echinops telfairi	ENSETEG00000007378	1 retrocopy	retro_etel_404,
Gorilla gorilla	ENSGGOG00000013892	1 retrocopy	retro_ggor_2983,
Macropus eugenii	ENSMEUG00000012636	1 retrocopy	retro_meug_778,
Microcebus murinus	ENSMICG00000005595	1 retrocopy	retro_mmur_1610,
Monodelphis domestica	ENSMODG00000017628	2 retrocopies	retro_mdom_1673, retro_mdom_561 ,
Oryctolagus cuniculus	ENSOCUG00000017351	1 retrocopy	retro_ocun_1575,
Otolemur garnettii	ENSOGAG00000013706	1 retrocopy	retro_ogar_206,
Ochotona princeps	ENSOPRG00000007310	1 retrocopy	retro_opri_574,
Pan troglodytes	ENSPTRG00000007038	1 retrocopy	retro_ptro_2949,