RetrogeneDB ID: retro_dnov_805

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_109232:4386..5065(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000024065
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SMYD2
• Ensembl ID: ENSDNOG00000014059
• Aliases: None
• Description: SET and MYND domain containing 2 [Source:HGNC Symbol;Acc:20982]

Sequence

>retro_dnov_805
AGTTGTTGCCCCAATGTGATCGTGACCTACAAGGGGACCCTGGTCAGAAGTAAGAGCGGTACAGGACATCAGCCCGGGAG
ACGAGGTGTTTACCAGCTACATCGACCTCCTATATCCAACCGAAGACAGGAATGACCGGCTCAGAGATTCCTACTTCTTC
ACCTGTGAGTGCCAGGAGTGCACCACCAAGGACAAGGATAAAGCCAAGGTGGAAATCCGGAAGCTCAGTGATCCCCCAAA
GGCAGAAGCCATCCGAGACATGGTCAGATACGCTCGCAATGTCATCGAGGAGTTCCGGAGGGCCAAGCACTACAAATCGC
CCAGTGAGCTGCTGGAGATCTGCGAGCTCAGCCAGGAGAAGATGAGCTCCATGTTCGAGGACAGTAACGTGTACATGCTG
CACATGATGTACCAGGCCATGGGCGTCTGTCTGTACATGCAGGACTGGGAAGGAGCCCTGCGATACGGACAGAAAATCAT
TAAGCCCTACAGTAACCATTATCCTTTGTACTCTCTCAACGTGGCCTCCATGTGGCTGAAGCTAGGAAGGTTGTACATGG
GCCTGGAAAACAAAGCTGCAGGAGAGCGAGCCCTGAAGAAGGCCCTCGCCATCATGGAAGTAGCTCACGGCAAAGACCAT
CCCTACGTTTCTGAGATCAGGCAGGAAATCGAGAGCCAC

Alignment

ORF - retro_dnov_805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.12 %
• Parental protein coverage: 52.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SCCPNVIVTYKGTL-AEVRAVQDISPGDEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAK
          SCCPNVIVTYKGTL..EVRAVQDISPGDEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAK
Retrocopy SCCPNVIVTYKGTL>SEVRAVQDISPGDEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAK

Parental  VEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSMFEDSNVYMLHMMYQA
          VEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSMFEDSNVYMLHMMYQA
Retrocopy VEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSMFEDSNVYMLHMMYQA

Parental  MGVCLYMQDWEGALRYGQKIIKPYSNHYPLYSLNVASMWLKLGRLYMGLENKAAGERALKKALAIMEVAH
          MGVCLYMQDWEGALRYGQKIIKPYSNHYPLYSLNVASMWLKLGRLYMGLENKAAGERALKKALAIMEVAH
Retrocopy MGVCLYMQDWEGALRYGQKIIKPYSNHYPLYSLNVASMWLKLGRLYMGLENKAAGERALKKALAIMEVAH

Parental  GKDHPYVSEIRQEIESH
          GKDHPYVSEIRQEIESH
Retrocopy GKDHPYVSEIRQEIESH

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	27.03 RPM
SRP012922_cerebellum	0.14 RPM	20.07 RPM
SRP012922_heart	0.00 RPM	72.39 RPM
SRP012922_kidney	0.27 RPM	31.76 RPM
SRP012922_liver	0.00 RPM	8.20 RPM
SRP012922_lung	0.15 RPM	42.92 RPM
SRP012922_quadricep_muscle	0.35 RPM	166.68 RPM
SRP012922_spleen	0.00 RPM	22.55 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_805 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014059	1 retrocopy	retro_dnov_805 ,
Felis catus	ENSFCAG00000018917	1 retrocopy	retro_fcat_1437,
Nomascus leucogenys	ENSNLEG00000014428	1 retrocopy	retro_nleu_1279,