RetrogeneDB ID: retro_mdom_391

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:371712912..371713761(+)
• Located in intron of: ENSMODG00000006383

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSRP1
• Ensembl ID: ENSMODG00000009868
• Aliases: None
• Description: nuclear speckle splicing regulatory protein 1 [Source:HGNC Symbol;Acc:25305]

Sequence

>retro_mdom_391
TTTGATGATAAAGAGGCATTTGTGACATCTGCTTATAAAAAGAAGCTTCAAGAGAGAGCTGAGGAAGCAGAGAGAGGACA
GCCACTGCCCTGGAAGCTCGTCTGGATGTGACCAAGCAGAAAGACCTCAGTGGATTTTATAGGCATCTTTTGAATCAAGC
AGTTGGAGAAGTGCCTGAATGCAGCCTTCGGGAAGCTAGTTCTAGGATAAAAGAGGAGAAGCCACGGGGTTATTCTGATG
AATTAAATCCAGACCACAGAGTCCCAGTCAATAGAGCTGTACCCAAAACCAAAGTGAAAGATGAAAACCCTGATGCAGAC
AGTGACCTTGATGTGGAGAGCAGTGAAGATGATGATAAAACTGAAGACAAGAGTTGATGGAGCCACAGGAATGAGAGCGG
CTACCAGAGTGAAAGAAGCCAGGCCCACTCCAGCTCCTCGGGGGAGGTCAGAGACCACCAGAGCCGGAGCCACACCAAGA
GCTCCAGGACAGTGACAAGAGACAGAGGTGACCAGCATCAGGACCTCACCCATGAGAGCTACATCAGGGAGCCTCACAGA
CATCCTGAAAGTGGTCACCATAAAGAAAAACCAGATCAGCAAAGGTCCAGGGAAGACAGCTATAAAAGACCACATCTACA
AGAGGCGAGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGATACACCCAGAGCACAGGCAGGAA
GAGGAAAGGGAGAAGCAGCCCTCCAGGGGATGAGAAAGGGCCAGGCCAAGAAACAGCGAAGAGCTTCGTGGTAAGGCGAA
GGGGGAGATCAGGGACAGGGGCAAAGGCCATTCCAAGGAGAGGAAGAGA

Alignment

ORF - retro_mdom_391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.82 %
• Parental protein coverage: 54.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FDDKEAFVTSAYKKKLQERAEE-AERERRAAALEARLDVTKQKDLSGFYRHLLNQAVGEEEVPECSLREA
          FDDKEAFVTSAY.KK......E...RER.A.ALEARLDVTKQKDLSGFYRHLLNQAVG..EVPECSLREA
Retrocopy FDDKEAFVTSAY-KKKLQERAE<GSRERTATALEARLDVTKQKDLSGFYRHLLNQAVG--EVPECSLREA

Parental  SSRIKEEKPRGYSDELNPDHRVPANRVVPKTRVKDENPDADSDLDVDSSEDDDKTEDKSRWSHRKESGHQ
          SSRIKEEKPRGYSDELNPDHRVP.NR.VPKT.VKDENPDADSDLDV.SSEDDDKTEDKS.WSHR.ESG.Q
Retrocopy SSRIKEEKPRGYSDELNPDHRVPVNRAVPKTKVKDENPDADSDLDVESSEDDDKTEDKS*WSHRNESGYQ

Parental  SERSQAHSSSSGEDRGHQSRSHTKSSRTVTRERGDQHQVRSHESHIREPDRRPESGHHKEKPDQHRSRED
          SERSQAHSSSSGE.R.HQSRSHTKSSRTVTR.RGDQHQ...HES.IREP.R.PESGHHKEKPDQ.RSRED
Retrocopy SERSQAHSSSSGEVRDHQSRSHTKSSRTVTRDRGDQHQDLTHESYIREPHRHPESGHHKEKPDQQRSRED

Parental  SN-KDHVHKRREQEDRERRERRMDREHRQEEEREKQPSKGRERARLRNSEEPRDEARGETRDRSKGHAEG
          S..KDH..KRRE..................E.R...........R......PR................G
Retrocopy SY>KDHIYKRREXXXXXXXXXXXXXXKIHPEHRQEE-EREKQPSRG*ERARPRNSEELRGKAKGEIRDRG

Parental  KRNGQEKCR
          K....E..R
Retrocopy KGHSKERKR

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	0.48 RPM	0.00 RPM
SRP007412_cerebellum	0.33 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	0.98 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_391 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_391 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009868	1 retrocopy	retro_mdom_391 ,
Pongo abelii	ENSPPYG00000008130	1 retrocopy	retro_pabe_457,
Pan troglodytes	ENSPTRG00000008957	1 retrocopy	retro_ptro_162,
Sarcophilus harrisii	ENSSHAG00000003513	1 retrocopy	retro_shar_342,