RetrogeneDB ID: retro_mdom_1248

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:97696149..97696704(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD13
• Ensembl ID: ENSMODG00000015721
• Aliases: None
• Description: potassium channel tetramerization domain containing 13 [Source:HGNC Symbol;Acc:22234]

Sequence

>retro_mdom_1248
CCCCACTGCCTTATCCCTATGGTGACATCTCTAGGGAGGGACAGCAGCTTCTGGCTAGCACCACTAAGCCAATGGTGAAG
CTGCTGCACCATCAAAGTAACAACAAATACTCCTTATACCAGCATATCAGGCAACAACCTACTAAAGAAAATTGAGCTGT
CCAATATGCTGGCATTGTGCTTCCTCAGGTGGCTGCTCTTTCCCAAAGATGTACTGGGTGATAAAATCTGCTGCTGGTGG
TCTTTCTAAGGACAGAGTTAAAAGATTGCCAAAGTCTGCTGTACCTCCATTGTCTATACCACTTATAAGAAGCAAACCAA
GATGAAATTCCCAGAGGCAAGGATCTTTGAAGATACATCAAATATCCTGATCTGCAAGACAACCCAGGGGTCTGACCCTA
CTCTTCTAGAGTCCACTTGGGGTACTGCTGGAGGAGGTGGGTCTTAGCAAAGAGAAGATTAAGATGAATGGGAGCATCAA
GTATGAAGGATCCATGTCAGATGGCATATTATTCATGATGAATGACCCCACTGTCAGCAGGTTGTCATCAAGGAC

Alignment

ORF - retro_mdom_1248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.52 %
• Parental protein coverage: 61.54 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLCLIPMVTS-PREEQQLLASTSKPVVKLLHNRSNNKYS-YTSTSDDNLLKNIELFDKLALRFHGRLLFL
          P.CLIPMVTS..RE.QQLLAST.KP.VKLLH..SNNKYS.YTS.S..NLLK.IEL...LAL.F...LLF.
Retrocopy PHCLIPMVTS<SREGQQLLASTTKPMVKLLHHQSNNKYS>YTSISGNNLLKKIELSNMLALCFLRWLLFP

Parental  KDVLGDEICCW-SFYGQGRKIAEVCCTSIVYATEKKQTKVEFPEARIFEETLNILIYETPRGPDPALLEA
          KDVLGD.ICCW.SF.GQ..KIA.VCCTSIVY.T.KKQTK..FPEARIFE.T.NILI..T..G.DP.LLE.
Retrocopy KDVLGDKICCWWSF*GQS*KIAKVCCTSIVYTTYKKQTKMKFPEARIFEDTSNILICKTTQGSDPTLLES

Parental  TGGAAGGGGAGRGEDEDGREHRVRRIHVRRHITHDERPHGQQAVFKD
          T.G.AGGGG....ED.D..EH.V.RIHVR.HI.HDE.PH.QQ.V.KD
Retrocopy TWGTAGGGGS*QRED*DEWEHQV*RIHVRWHIIHDE*PHCQQVVIKD

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_1248 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1248 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000015721	1 retrocopy	retro_mdom_1248 ,
Monodelphis domestica	ENSMODG00000019235	1 retrocopy	retro_mdom_1565,