RetrogeneDB ID: retro_mdom_345

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:236379005..236379466(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NHP2
• Ensembl ID: ENSMODG00000004231
• Aliases: None
• Description: NHP2 ribonucleoprotein [Source:HGNC Symbol;Acc:14377]

Sequence

>retro_mdom_345
ATGACTGAAGTAAACTGGGAAGTGGAGTAGTCAGAGGTAGCGCTGGAGACTTCTGGGGAACCTGAGCCCGTGTAGGAGGA
GATACTGGGGAACCTGAACCCAAGCGCGCAGTACCTGGCCTCCTGCCGCTCAATGCGGAAGCTATACATATCCATCAAGA
AAGCTGTGAAGCAGAAGCAGATTGGGCGATGAGTGAAGAAAGTTCAGAAATTCCTCAATAAAGAAGAAAAGGGCATTATG
CTTTTGGCTAGGGACACACTAAACATTGAGGAATACTGCCACCTACCCATTACGTGTGAGGATCTGAGCATGGCATATGC
CTATGTTCCCACAAAAACAGATCTGGGAGCAGTTGCTGGCTCTAAGCGCCCAACGTTATGATCATGATTAATCCACATGA
AGACTACCAAGCTACATATAATGATTGCCTGGGGGAAGTAGAATCTCTTCCTGTTGCCTTG

Alignment

ORF - retro_mdom_345 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTKVKREVEESEAAPETSAEPERTYEEMLANLNPIAQPLASRRLTRKLYKCIKKAVKQKQIRRGVKEVQK
          MT.V..EVE.SE.A.ETS.EPE...EE.L.NLNP.AQ.LAS.R..RKLY..IKKAVKQKQI.R.VK.VQK
Retrocopy MTEVNWEVE*SEVALETSGEPEPV*EEILGNLNPSAQYLASCRSMRKLYISIKKAVKQKQIGR*VKKVQK

Parental  FLNKGEKGIMVLAGDTLPIEVYCHLPIMCEDLSMPYAYVPSKTDLGAAAGSKRPT-CVIMIKPHEDYQAT
          FLNK.EKGIM.LA.DTL.IE.YCHLPI.CEDLSM.YAYVP.KTDLGA.AGSKRPT...IMI.PHEDYQAT
Retrocopy FLNKEEKGIMLLARDTLNIEEYCHLPITCEDLSMAYAYVPTKTDLGAVAGSKRPT<VMIMINPHEDYQAT

Parental  YDECLEEVESLPVPL
          Y..CL.EVESLPV.L
Retrocopy YNDCLGEVESLPVAL

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	111.21 RPM
SRP007412_cerebellum	0.00 RPM	117.85 RPM
SRP007412_heart	0.00 RPM	65.99 RPM
SRP007412_kidney	0.00 RPM	235.71 RPM
SRP007412_liver	0.00 RPM	136.45 RPM
SRP007412_testis	0.00 RPM	154.20 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_345 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_345 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012244	1 retrocopy	retro_cjac_264,
Homo sapiens	ENSG00000145912	2 retrocopies	retro_hsap_3712, retro_hsap_611,
Gorilla gorilla	ENSGGOG00000000015	1 retrocopy	retro_ggor_2509,
Macropus eugenii	ENSMEUG00000003839	2 retrocopies	retro_meug_285, retro_meug_320,
Macaca mulatta	ENSMMUG00000018757	1 retrocopy	retro_mmul_1702,
Monodelphis domestica	ENSMODG00000004231	1 retrocopy	retro_mdom_345 ,
Mus musculus	ENSMUSG00000001056	1 retrocopy	retro_mmus_565,
Oryctolagus cuniculus	ENSOCUG00000016057	1 retrocopy	retro_ocun_151,
Ochotona princeps	ENSOPRG00000007907	3 retrocopies	retro_opri_305, retro_opri_421, retro_opri_810,
Pongo abelii	ENSPPYG00000016105	3 retrocopies	retro_pabe_1704, retro_pabe_3143, retro_pabe_481,
Rattus norvegicus	ENSRNOG00000004247	2 retrocopies	retro_rnor_1436, retro_rnor_2198,
Sus scrofa	ENSSSCG00000014032	1 retrocopy	retro_sscr_407,