RetrogeneDB ID: retro_mdom_932

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:488150660..488151212(-)
• Located in intron of: ENSMODG00000005063

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNMT
• Ensembl ID: ENSMODG00000001168
• Aliases: None
• Description: histamine N-methyltransferase [Source:HGNC Symbol;Acc:5028]

Sequence

>retro_mdom_932
AAGAACGTAAAGTTTGCTTGGCATCAGGAGACATCATCTGAATATCAAAGTAGAATAATAGAGAAAAAGGAGCTTCAGAA
ATGGAACTTTATTCACATGATTCAGATGCTGTATTATGTAAAAGATATCCCAACTACTCTGAAATTTTTCCACAGTCTCC
TGGATACTGAGGGCAAGATTCTTATTATTCTTGTGTCAGGAATGAGTGGTTGGGACAAACTGTGGAAGAAGTATGGATCC
CGCTTACCCCAAAATGATCTCTGCCTCTATGTGTCATCCTCTGACATCACTCAAACCCTAGAAACTTTGGGAATTAAATA
TGAATGCTTTGAACTTCTATCTACTATGGATATATCAGATTGCTTTGTTGAAGGCAATGAAAAAGGGGAGTTACTGCTGG
ACTTTTTAACAGAAACCTGCCACTTTAGCCAAACTGCGCCACCTGATCTCAAAGCTGAGATTATCGAAGACCTTCAAAGG
CCAGGATTCAGTGTAAAAGAAAGGGGAAAGACCCTTTTTCAGAATCACTTAAGTTTCATAGTTGTTGAAGCA

Alignment

ORF - retro_mdom_932 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.91 %
• Parental protein coverage: 63.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNVKFAWHQETSSEYQSRIMEKKELQKWNFIHMIQVQIFGFLRNFQIKRFFYRFYPMLSLSFDIKVDEVL
          KNVKFAWHQETSSEYQSRI.EKKELQKWNFIHM...Q.............F..F...L.....I....V.
Retrocopy KNVKFAWHQETSSEYQSRIIEKKELQKWNFIHM--IQMLYYVKDIPTTLKF--FHSLLDTEGKILIILVS

Parental  RMSGWDKLWKKYGSRLPQNDLCLYVSSSDITQTLETLGIKYECFELLSTMDISDCFVEGNEKGELLLDFL
          .MSGWDKLWKKYGSRLPQNDLCLYVSSSDITQTLETLGIKYECFELLSTMDISDCFVEGNEKGELLLDFL
Retrocopy GMSGWDKLWKKYGSRLPQNDLCLYVSSSDITQTLETLGIKYECFELLSTMDISDCFVEGNEKGELLLDFL

Parental  TETCHFSQTAPPDLKAEIIEDLQRPGFTVKERGKTLFQNHLSFIVVEA
          TETCHFSQTAPPDLKAEIIEDLQRPGF.VKERGKTLFQNHLSFIVVEA
Retrocopy TETCHFSQTAPPDLKAEIIEDLQRPGFSVKERGKTLFQNHLSFIVVEA

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_932 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_932 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015340	1 retrocopy	retro_dnov_1969,
Myotis lucifugus	ENSMLUG00000015156	2 retrocopies	retro_mluc_1174, retro_mluc_1417,
Monodelphis domestica	ENSMODG00000001168	1 retrocopy	retro_mdom_932 ,
Tursiops truncatus	ENSTTRG00000012879	1 retrocopy	retro_ttru_1560,