RetrogeneDB ID: retro_dnov_1969

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_39510:13218..13687(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNMT
• Ensembl ID: ENSDNOG00000015340
• Aliases: None
• Description: histamine N-methyltransferase [Source:HGNC Symbol;Acc:5028]

Sequence

>retro_dnov_1969
GTAGCCAAGACATCAAACCTTGAGAACATAAAGCTTGCTTGGCATAAGGAGACATCATCTGAATATCAAAATAGGATGAT
GGAGAAAAAAGAGTTTCAAAAGTGGGACTTTATTCACATGGTTCAGATGCTGTGTTATGTAAAAGTCATCCCAGCTACCC
TGAAATTCTTCCATGGTCTCTTAGCTACCAATTCTCCTTGTTCTTGTATTGGGAACCAGTGGCTGGGACAAGCTGTGGAA
AAAGTATGGATCCCACTTACTTTGGGATGACCTTTACTAGTACATTTCATCATCTGACCCCACGCAGATGCTGGACAACT
TGGGGATTAAGCATGAATGTTACAAACCTCTGTCCACCGTGGATGTATCTGACTGTTTTATTGATGGCAATGTAAATGGA
GACTTGCTCTGGGTTTTTTTGACAGAAACCCTCAACTTTAGCACTACAGCACTACATGATCTCAAAGCA

Alignment

ORF - retro_dnov_1969 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.38 %
• Parental protein coverage: 61.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAKTSNLENIKFAWHKETSSEYQNKMMEKKEFQKWDFIHMIQMLYYVKDIPATLKFFHGLLAASAK-ILI
          VAKTSNLENIK.AWHKETSSEYQN.MMEKKEFQKWDFIHM.QML.YVK.IPATLKFFHGLLA......L.
Retrocopy VAKTSNLENIKLAWHKETSSEYQNRMMEKKEFQKWDFIHMVQMLCYVKVIPATLKFFHGLLATNSP>VLV

Parental  ILVSGTSGWDKLWKKYGSRLPRDDFCLYITSSDLMQTLDNLGIKYNCYDLPSTMDISDCFIDGNENGDLL
          ...SG...WDKLWKKYGS.L..DD...YI.SSD..Q.LDNLGIK..CY...ST.D.SDCFIDGN.NGDLL
Retrocopy LGTSG---WDKLWKKYGSHLLWDDLY*YISSSDPTQMLDNLGIKHECYKPLSTVDVSDCFIDGNVNGDLL

Parental  WDFLTETLNFNRTAPPDLKA
          W.FLTETLNF..TA..DLKA
Retrocopy WVFLTETLNFSTTALHDLKA

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
SRP012922_ascending_colon	0.00 RPM	3.50 RPM
SRP012922_cerebellum	0.00 RPM	7.70 RPM
SRP012922_heart	0.00 RPM	0.70 RPM
SRP012922_kidney	0.00 RPM	1.37 RPM
SRP012922_liver	0.00 RPM	2.94 RPM
SRP012922_lung	0.00 RPM	5.04 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.17 RPM
SRP012922_spleen	0.00 RPM	26.44 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_1969 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus 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,