RetrogeneDB ID: retro_mdom_1223

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:18362341..18362648(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMTM4
• Ensembl ID: ENSMODG00000006885
• Aliases: None
• Description: CKLF-like MARVEL transmembrane domain containing 4 [Source:HGNC Symbol;Acc:19175]

Sequence

>retro_mdom_1223
TTCTTTGACTTTGTGAACTGTAATATTTCCGTAAGCACTGGAGTTTTGTTGTTTATGCTCAGTCTCAATCTTCACACAAG
GAAACACAGTTCAACTGGAACATTACATATTTGGGCAACACTGGACTCAGCGCCTTCTTTATTGCTTGCTTCGATGGTAC
GGACTGCTTTGAATCATAAAACTAGAGCAGAAATCCTGCCGTGGTTTTTGGCTTTTTGGCAACAGCGGTGTATGCCCTAA
CGTTCTTGGTTGTGCAGGAAAGAAAAATGAACATTCCAACCAGAGGACCAATGAATTCATCTGTGCG

Alignment

ORF - retro_mdom_1223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.14 %
• Parental protein coverage: 50.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FFEFVSCSAFVITGVLLLMFSLNLHTRI-PQINWNITDLVNTGLSTFFFF-IASIVLAALNHKAGAEIA-
          FF.FV.C...V.TGVLL.M.SLNLHTR...Q.NWNIT.L.NTGLS..FF...AS.V..ALNHK..AEI..
Retrocopy FFDFVNCNISVSTGVLLFMLSLNLHTRK<TQFNWNITYLGNTGLSA-FFI>LASMVRTALNHKTRAEIL<

Parental  AVVFGFLATAVYAANTFLAVQKWRMNI-RQQSTNEYIRA
          AVVFGFLATAVYA..TFL.VQ...MNI...Q.TNE.I.A
Retrocopy AVVFGFLATAVYAL-TFLVVQERKMNI<SNQRTNEFICA

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_1223 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1223 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000006885	1 retrocopy	retro_mdom_1223 ,