RetrogeneDB ID: retro_dnov_2139

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_50765:12794..13027(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPC1
• Ensembl ID: ENSDNOG00000001205
• Aliases: None
• Description: mitochondrial pyruvate carrier 1 [Source:HGNC Symbol;Acc:21606]

Sequence

>retro_dnov_2139
GCGGGCGCGCTGGGGCGGGAAGCCGCGGACTGTGTCCCACGCAAGGAGCTCGGGACTACCTTCTGAGCATGCACTTTTGG
GGGCCAGTAGCCAACTGGGTTCCTCCCACTGCTGCCATCAATGACAGGAAAAAGTCTCCCGAGATGATCAGCGGTCGGAT
GACATTTGCCCTTTGCTGTTATTCTTCGACATTCCTGAGATTTGCCTACAAGGTACAACCTCGAAACTGGCTT

Alignment

ORF - retro_dnov_2139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.22 %
• Parental protein coverage: 71.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGALVRKAADYVRSKEF-RDYLMS-HFWGPVANWGLPIAAINDMNKSPEIISGRMTFALCCYSVAFMRFA
          AGAL.R.AAD.V..KE..RDYL.S.HFWGPVANW..P.AAIND..KSPE.ISGRMTFALCCYS..F.RFA
Retrocopy AGALGREAADCVPRKEL<RDYLLSMHFWGPVANWVPPTAAINDRKKSPEMISGRMTFALCCYSSTFLRFA

Parental  YKVQPRNWL
          YKVQPRNWL
Retrocopy YKVQPRNWL

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	17.11 RPM
SRP012922_cerebellum	0.00 RPM	29.01 RPM
SRP012922_heart	0.00 RPM	99.54 RPM
SRP012922_kidney	0.00 RPM	105.96 RPM
SRP012922_liver	0.00 RPM	33.75 RPM
SRP012922_lung	0.00 RPM	47.65 RPM
SRP012922_quadricep_muscle	0.00 RPM	180.53 RPM
SRP012922_spleen	0.00 RPM	18.08 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_2139 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027879	1 retrocopy	retro_btau_43,
Callithrix jacchus	ENSCJAG00000012552	2 retrocopies	retro_cjac_2102, retro_cjac_4053,
Dasypus novemcinctus	ENSDNOG00000001205	1 retrocopy	retro_dnov_2139 ,
Homo sapiens	ENSG00000060762	1 retrocopy	retro_hsap_4675,
Myotis lucifugus	ENSMLUG00000000583	1 retrocopy	retro_mluc_28,
Mus musculus	ENSMUSG00000023861	3 retrocopies	retro_mmus_2037, retro_mmus_3420, retro_mmus_979,
Ornithorhynchus anatinus	ENSOANG00000004153	1 retrocopy	retro_oana_45,
Pongo abelii	ENSPPYG00000017166	1 retrocopy	retro_pabe_17,
Rattus norvegicus	ENSRNOG00000012415	3 retrocopies	retro_rnor_1111, retro_rnor_2632, retro_rnor_296,
Tursiops truncatus	ENSTTRG00000004456	1 retrocopy	retro_ttru_663,