RetrogeneDB ID: retro_mdom_562

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:316535904..316536246(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL47
• Ensembl ID: ENSMODG00000021301
• Aliases: None
• Description: mitochondrial ribosomal protein L47 [Source:HGNC Symbol;Acc:16652]

Sequence

>retro_mdom_562
TTTACTTTCAGTTTGTTAATCAAGATTAAAGCCAACATCAGTCCCCTCCGTCAATATAAATTAATTCATACTACTTTGTC
AAGAAAATAACTAGAATTTTTTTGATGATCCAAAAATTGGAGAGCAGAAATTGTCAAATTAGGTGCTACATGGACCCATG
AACACTTAAGATGCAAGAGTAATGAAGATTTGCATAAGCTTTCGTAAGTACTACTGAAAGAAAGAAACATGATTCTCACA
TTAGAGCAGGAGGCCAAAAGACAAAGTTTGCCAATGCCAAGTCTAGAGCAATTAGAAAAGGTGATAGAATCCCTGGATGT
TTTAGATAAAGTTATTCAGGAA

Alignment

ORF - retro_mdom_562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 51.34 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTFSLLNKIRANINPFHQYKLIHTTLSRKGLEEFFDDPKNWGAETVKSGAAWTHEQLRCKSNEDLHKLWY
          FTFSLL.KI.ANI.P..QYKLIHTTLSRK.L.EFF...KNW.AE.VK.GA.WTHE.LRCKSNEDLHKL..
Retrocopy FTFSLLIKIKANISPLRQYKLIHTTLSRK*L-EFF**SKNWRAEIVKLGATWTHEHLRCKSNEDLHKLS*

Parental  VLLKERNMLLTLEQEAKRQRLPMPSPERLEKVTESMDALDKVVQE
          VLLKERNM.LTLEQEAKRQ.LPMPS.E.LEKV.ES.D.LDKV.QE
Retrocopy VLLKERNMILTLEQEAKRQSLPMPSLEQLEKVIESLDVLDKVIQE

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_562 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_562 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011380	1 retrocopy	retro_cfam_1085,
Cavia porcellus	ENSCPOG00000002312	2 retrocopies	retro_cpor_1219, retro_cpor_885,
Felis catus	ENSFCAG00000031548	1 retrocopy	retro_fcat_235,
Macropus eugenii	ENSMEUG00000012649	2 retrocopies	retro_meug_1039, retro_meug_146,
Monodelphis domestica	ENSMODG00000021301	3 retrocopies	retro_mdom_1361, retro_mdom_1879, retro_mdom_562 ,
Mustela putorius furo	ENSMPUG00000017214	1 retrocopy	retro_mputfur_495,
Mus musculus	ENSMUSG00000037531	3 retrocopies	retro_mmus_1976, retro_mmus_1986, retro_mmus_2753,
Otolemur garnettii	ENSOGAG00000016957	2 retrocopies	retro_ogar_1900, retro_ogar_3015,
Pteropus vampyrus	ENSPVAG00000004284	1 retrocopy	retro_pvam_150,
Rattus norvegicus	ENSRNOG00000011639	2 retrocopies	retro_rnor_1829, retro_rnor_2523,
Sorex araneus	ENSSARG00000006898	2 retrocopies	retro_sara_269, retro_sara_721,
Tursiops truncatus	ENSTTRG00000008909	1 retrocopy	retro_ttru_420,