RetrogeneDB ID: retro_mdom_1457

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:144036924..144037303(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM199
• Ensembl ID: ENSMODG00000019239
• Aliases: None
• Description: transmembrane protein 199 [Source:HGNC Symbol;Acc:18085]

Sequence

>retro_mdom_1457
ATTGAGCTGCATGGGAGCTTGAGGAAGCTGGTCTTCCTTCATGGGCTCCTGAAAGGCAGTGCAAGTGCAGTCTATCTCCC
CAAGATTGTGAAACCCCACCAGGAATCCATAGCTGATCTCCCACCTGGAGCAGATCAAAGTACAATTGGCCAGTGAGTAA
TATTAGCCAATCGCCTGAAATGTTTCCTGCCAGTCTTGGAGGCAGAATGAGACTCTGGTTGACTTAGGATGCCAAAAGAG
GTCATTGAAGGCAGTGGTCATCACCATCTTCAACTGCATCGTCGTTATGGCAGTAGCTTTTCCCTGCATCTAACTAGGAA
GTCAGTACATCATCTCTGAAATGACAGAGAGGGTGCTGGCTGCAGTGATTATTGTTGCC

Alignment

ORF - retro_mdom_1457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 61.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LELHQHLRQQGSSVFLHELLEGSE--IYLPKIVKP-PRNPELVARLEKIKVQLANEEYSRITRNVSCQAS
          .ELH..LR.....VFLH.LL.GS....YLPKIVKP..RNP.L...LE.IKVQLA.E.Y..I..NVSCQ..
Retrocopy IELHGSLRKL---VFLHGLLKGSASAVYLPKIVKP>TRNP*LISHLEQIKVQLASE*Y*PIA*NVSCQSW

Parental  KQSGTLAGLGQQVRSAKALVINIFNFFVTVAAAFTCTYLGSQYIFSEMTGRVLAAVIVAS
          .Q..TL..LG.Q.RS.KA.VI.IFN..V..A.AF.C..LGSQYI.SEMT.RVLAAVI...
Retrocopy RQNETLVDLGCQKRSLKAVVITIFNCIVVMAVAFPCI*LGSQYIISEMTERVLAAVIIVA

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_1457 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1457 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
Myotis lucifugus	ENSMLUG00000012307	1 retrocopy	retro_mluc_1156,
Monodelphis domestica	ENSMODG00000019239	1 retrocopy	retro_mdom_1457 ,
Otolemur garnettii	ENSOGAG00000003338	1 retrocopy	retro_ogar_801,
Tarsius syrichta	ENSTSYG00000014137	1 retrocopy	retro_tsyr_845,