RetrogeneDB ID: retro_mdom_511

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:105539949..105540556(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC25
• Ensembl ID: ENSMODG00000015976
• Aliases: None
• Description: coiled-coil domain containing 25 [Source:HGNC Symbol;Acc:25591]

Sequence

>retro_mdom_511
ATGTTCTACTTCACCATCCATGCTGATTCATCTATTTACATCATTTATGTGGGAAAAGATGAATATGAAAAAGAAGATCT
AATAAAATATGGCTGGCTAAAAGATTTTTGGTTTTATGTGGACAAACCGTCTTCAGCCCACATGTACCTTTAGCTACACA
AGGGGGAAAGGATAGAAGATATTCCAGAGGATGTGCTAATGGACTGGGTACACTTTGTGAAAGCTAATACTATTCAAGGC
TACAAGATGAACAATGTAAATGTTGTATATATACCATGATCCAACCTGAAGAAAATAGCAGACATGGATGTGGGCAGGGG
ATTTCACAGGCAAAGAATATGAAAATTTTAACAATAGAGAAGAAAGCAAATGAGATTCTGAATTCATTAGAAAAGACTAA
AATGGAGCAATTCCCAGACTTAGCAATAGAGGAAAAAGCTGAGACAGATAGGAAAAGAATAAGAACAAAGTCCAGATCCA
AGAAATGAAGAAGAAAGAGGAAGGGAAATTGAAGAAGAAAATAAATACAATTAGGTGTTATTCTTCACTAATGAAGTCTG
AGAATATGTTTTTGAATCACAATTGCAATGATTCACATGAATTCATG

Alignment

ORF - retro_mdom_511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.71 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFYFTSHADSSVYTIYMGKDKYENEDLIKYGWPEDIWFHVDKLSSAHVYLRLHKGERIEDIPKEVLMDCA
          .FYFT.HADSS.Y.IY.GKD.YE.EDLIKYGW..D.WF.VDK.SSAH.YL.LHKGERIEDIP..VLMD..
Retrocopy MFYFTIHADSSIYIIYVGKDEYEKEDLIKYGWLKDFWFYVDKPSSAHMYL*LHKGERIEDIPEDVLMDWV

Parental  HLVKANSIQGCKMNNVNVVYTPWSNLKKTADMDVGQIGFHRQ-KDVKIVTVEKKVNEILNRLEKTKLERF
          H.VKAN.IQG.KMNNVNVVY.P.SNLKK.ADMDVG..GFHRQ.K..KI.T.EKK.NEILN.LEKTK.E.F
Retrocopy HFVKANTIQGYKMNNVNVVYIP*SNLKKIADMDVGR-GFHRQ<KNMKILTIEKKANEILNSLEKTKMEQF

Parental  PDLAAEKECR-DREERNEKKAQIQEMKRKEKEELKKKKEMDELRSYSSLMKSENMSSNQDGNDSDEFM
          PDLA.E.....DR.E.N..K.QIQEMK.KE...LKKK......R.YSSLMKSENM..N...NDS.EFM
Retrocopy PDLAIEEKAE<DR*EKNKNKVQIQEMKKKEEGKLKKK--INTIRCYSSLMKSENMFLNHNCNDSHEFM

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	205.97 RPM
SRP007412_cerebellum	0.00 RPM	153.76 RPM
SRP007412_heart	0.00 RPM	112.24 RPM
SRP007412_kidney	0.00 RPM	185.67 RPM
SRP007412_liver	0.00 RPM	173.20 RPM
SRP007412_testis	0.00 RPM	452.39 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_511 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_511 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012971	2 retrocopies	retro_chof_2254, retro_chof_847,
Dipodomys ordii	ENSDORG00000006595	1 retrocopy	retro_dord_491,
Echinops telfairi	ENSETEG00000006478	1 retrocopy	retro_etel_434,
Homo sapiens	ENSG00000147419	1 retrocopy	retro_hsap_1701,
Gorilla gorilla	ENSGGOG00000009685	1 retrocopy	retro_ggor_1274,
Monodelphis domestica	ENSMODG00000015976	1 retrocopy	retro_mdom_511 ,
Pongo abelii	ENSPPYG00000018468	2 retrocopies	retro_pabe_1364, retro_pabe_477,
Pan troglodytes	ENSPTRG00000020109	1 retrocopy	retro_ptro_141,
Tarsius syrichta	ENSTSYG00000000732	1 retrocopy	retro_tsyr_1364,