RetrogeneDB ID: retro_mdom_338

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:210710631..210711358(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000017547
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RSU1
• Ensembl ID: ENSMODG00000009942
• Aliases: None
• Description: Ras suppressor protein 1 [Source:HGNC Symbol;Acc:10464]

Sequence

>retro_mdom_338
ATGTCCATGTCTTTGAAGAAGCTGGTGGAGGAAAGTCCGGAGAAGAACCAGCCCGAGGTGGACATGTGTCACCGCGACAT
CTCCAACATGCTGGAAGTCCATGGCTTGTTTACTTTATCCCACATTTCACAACTGGTTCTCAGCCACAACAAGCTAACAA
CTGTGCCAAAACATGGTAGAACTGAAGAATCTGGAAGTACTGAACTTTTTCAATAACCAGATTGAAGAGCTGCCCACACA
GTTCAGCAGCCTCCAGAAACTCAAACACCTGAACCTTGGTATGAACAGGCTAAATACTTTGCCCCGAGGATTTGGCTCCT
TACCAACCCTGGAGGTCCTTGACTTGAGTTATAACAACTTGAATGAAAATTCTCTTCCTGGAAACTTCTACCTTACCACC
CTGTGTGCACTTTATCGAAGTGACAACGATTTTGAAATCCTGCCACCAGATATTGGGAAGTTCACAAAGTTGCAGATAGT
CAGCCTTAGGGATAATGACATGATATCACTGCCAAAAGAAACTGGAGAACTTACGCAACTGAAAGAACTACACATCCAAG
GGAACCCCCTGACTGTCCTTCCCCCTGAGCTTGGAAACTTGGATTTAACAGGACAGAAGCAGGTCTTGAACGCAGAAAAT
CATCCCTGGGTTAAGCCAATTGCTGACCAGTTCCAGCTCAGAGTGTCTCATGTCTTTGAATACATCCGTTCTGAAACATA
CAAGTAC

Alignment

ORF - retro_mdom_338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.98 %
• Parental protein coverage: 94.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKSLKKLVEESREKNQPEVDMCDRGISNMLDVHGLFTLSHITQLVLSHNKLTTVPP-NVAELKNLEVLN
          MS.SLKKLVEES.EKNQPEVDMC.R.ISNML.VHGLFTLSHI.QLVLSHNKL.T..P.N..ELKNLEVLN
Retrocopy MSMSLKKLVEESPEKNQPEVDMCHRDISNMLEVHGLFTLSHISQLVLSHNKL-TTVP>NMVELKNLEVLN

Parental  FFNNQIEELPTQISSLQKLKHLNLGMNRLNTLPRGFGSLPALEVLDLTYNNLNENSLPGNFFYLTTLRAL
          FFNNQIEELPTQ.SSLQKLKHLNLGMNRLNTLPRGFGSLP.LEVLDL.YNNLNENSLPGNF.YLTTL.AL
Retrocopy FFNNQIEELPTQFSSLQKLKHLNLGMNRLNTLPRGFGSLPTLEVLDLSYNNLNENSLPGNF-YLTTLCAL

Parental  YLSDNDFEILPPDIGKLTKLQILSLRDNDLISLPKETGELTQLKELHIQGNRLTVLPPELGNLDLTGQKQ
          Y.SDNDFEILPPDIGK.TKLQI.SLRDND.ISLPKETGELTQLKELHIQGN.LTVLPPELGNLDLTGQKQ
Retrocopy YRSDNDFEILPPDIGKFTKLQIVSLRDNDMISLPKETGELTQLKELHIQGNPLTVLPPELGNLDLTGQKQ

Parental  VFKAENNPWVTPIADQFQLGVSHVFEYIRSETYKY
          V..AEN.PWV.PIADQFQL.VSHVFEYIRSETYKY
Retrocopy VLNAENHPWVKPIADQFQLRVSHVFEYIRSETYKY

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	4.77 RPM	0.00 RPM
SRP007412_cerebellum	2.94 RPM	0.00 RPM
SRP007412_heart	1.59 RPM	0.00 RPM
SRP007412_kidney	2.63 RPM	0.00 RPM
SRP007412_liver	3.52 RPM	0.00 RPM
SRP007412_testis	1.38 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_338 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_338 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000148484	1 retrocopy	retro_hsap_575,
Gorilla gorilla	ENSGGOG00000028048	1 retrocopy	retro_ggor_512,
Macropus eugenii	ENSMEUG00000006702	1 retrocopy	retro_meug_2092,
Macaca mulatta	ENSMMUG00000016067	1 retrocopy	retro_mmul_712,
Monodelphis domestica	ENSMODG00000009942	1 retrocopy	retro_mdom_338 ,
Monodelphis domestica	ENSMODG00000012729	1 retrocopy	retro_mdom_1822,
Nomascus leucogenys	ENSNLEG00000012444	1 retrocopy	retro_nleu_462,
Pongo abelii	ENSPPYG00000002120	1 retrocopy	retro_pabe_611,
Pan troglodytes	ENSPTRG00000002325	1 retrocopy	retro_ptro_425,
Tarsius syrichta	ENSTSYG00000002386	1 retrocopy	retro_tsyr_730,