RetrogeneDB ID: retro_mdom_426

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:487553676..487554107(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18B
• Ensembl ID: ENSMODG00000015933
• Aliases: None
• Description: mitochondrial ribosomal protein S18B [Source:HGNC Symbol;Acc:14516]

Sequence

>retro_mdom_426
TGCATTTATGGAAACAAAGTTGCTAGGAACCCTTGACCCTTCTGTTGGGACCAGAACCTTTGCAAGGACTTCAGAAATGT
GAGGCTGACAGAGCAATTTGTCTTTGCTAACATAGGTATCATTTTCCATGCCTCATATACAGTTGTCTGTCTATATGAAG
GTTTGACAGAGACTGTCCTGAAGGCCAGACACCATGGTTTCTCTGTTACCCCATCCCCCATGAAAAAGCCACAGAATACT
CATTTCAGCAACTTTGGGGGGACTGTGGGCTTTACTTCAATGGTTCCTGCCCTTGAAGCAAATGTGTCCTGGTATCCATG
GTATATTTGGCAGCAGTCATCTAAGAGAGAACTGAGCCACCTTCAATATCTGCATCAGGTCATCTTAGGGTTGAGAGTGG
ACTTCCACCAGAGATACTCATAGTTCCATCT

Alignment

ORF - retro_mdom_426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.08 %
• Parental protein coverage: 61.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CIRGNKVSGNPCPICRDQKLHVDFRNVKLLEQFVCAHTGVIFHAPYTGVCMKQHKKLTEAILKARDQGLL
          CI.GNKV..NP.P.C.DQ.L..DFRNV.L.EQFV.A..G.IFHA.YT.VC......LTE..LKAR..G..
Retrocopy CIYGNKVARNP*PFCWDQNLCKDFRNVRLTEQFVFANIGIIFHASYTVVCL--YEGLTETVLKARHHGFS

Parental  SYHIPLVQPRDTDFSNSHGAVGLTPMAPALAAGTAWYPWYTWQQPPERELARLRRLYQ-GHLKEESGPPP
          ....P...P..T.FSN..G.VG.T.M.PAL.A...WYPWY.WQQ...REL..L..L.Q.GHL..ESG.PP
Retrocopy VTPSPMKKPQNTHFSNFGGTVGFTSMVPALEANVSWYPWYIWQQSSKRELSHLQYLHQ<GHLRVESGLPP

Parental  EMMPIVPS
          E...IVPS
Retrocopy EIL-IVPS

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_426 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_426 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 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005581	1 retrocopy	retro_chof_505,
Macropus eugenii	ENSMEUG00000012457	10 retrocopies	retro_meug_1183, retro_meug_2004, retro_meug_2124, retro_meug_215, retro_meug_610, retro_meug_648, retro_meug_696, retro_meug_712, retro_meug_717, retro_meug_734,
Macaca mulatta	ENSMMUG00000006525	1 retrocopy	retro_mmul_900,
Monodelphis domestica	ENSMODG00000015933	1 retrocopy	retro_mdom_426 ,
Mus musculus	ENSMUSG00000024436	1 retrocopy	retro_mmus_2036,
Nomascus leucogenys	ENSNLEG00000005224	1 retrocopy	retro_nleu_1811,
Oryctolagus cuniculus	ENSOCUG00000002149	2 retrocopies	retro_ocun_1307, retro_ocun_1641,
Pongo abelii	ENSPPYG00000016412	1 retrocopy	retro_pabe_2050,
Pan troglodytes	ENSPTRG00000017932	1 retrocopy	retro_ptro_1648,
Rattus norvegicus	ENSRNOG00000000804	1 retrocopy	retro_rnor_1328,
Ictidomys tridecemlineatus	ENSSTOG00000011853	1 retrocopy	retro_itri_254,
Tarsius syrichta	ENSTSYG00000003333	1 retrocopy	retro_tsyr_1769,