RetrogeneDB ID: retro_dnov_823

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_111105:43013..43597(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT5
• Ensembl ID: ENSDNOG00000004979
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 5 [Source:HGNC Symbol;Acc:20886]

Sequence

>retro_dnov_823
ATGCTGCTGTCGCTGGTGCTGCACACGTACTCGATGCGCTACGTGCTGCCGGCCGCCGTGCTGCTGGGCTCGGCGTCCAC
CTACGTGCTGGCCTGGGGCGCCTGGCGCCTGCTGTCCTGCCTGCTGCCCGCGCGCTGCTACCGCGCGCTCGACGACCGCC
TCTACTGCGTCTACCAGAGCATGATGCTCTTCTTCTTCGAGAACTACACCGGCGTGCAGATATTGCTATATGGGGATTTG
CCAAAAAATAAAGAAAATATAATATATTTATCAAATCATCAAAGCACAGTTGACTGGATCGTTGCTGACATTTTGGCCAT
CAGACAGAACGTGCTGGGCCACGTGCGCTACGTTTTGAAGGACGGGCTGAAGTGGCTTCCACTGTACGGGTGTTATTTTT
CTCAGCATGGAGGAATCTATGTAAAGCGAAGTGCCAATTTAATGAAAAAGAAATGCGAAACAAGCTGCAGAGCCACATGA
AAGCAGGAACTCCAATGTTTCTTGTGATTTTTCCAGAGGGAACAAGGTATAATCCGGAACTAACAAAAGTCATTTCAGCT
AGTCAAACATTTGCTGCTCAAGAA

Alignment

ORF - retro_dnov_823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.39 %
• Parental protein coverage: 53.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLLSLVLLASSLRRVLPAAVLLGSAPTYVLAWGAWRLLSCLLPARCYRALDDRLYCVYQSMVLFFFENYT
          .LLSLVL...S.R.VLPAAVLLGSA.TYVLAWGAWRLLSCLLPARCYRALDDRLYCVYQSM.LFFFENYT
Retrocopy MLLSLVLHTYSMRYVLPAAVLLGSASTYVLAWGAWRLLSCLLPARCYRALDDRLYCVYQSMMLFFFENYT

Parental  GVQILLYGDLPKNKENIIYLSNHQSTVDWIVADILAIRQNALGHVRYVLKDGLKWLPLYGCYFSQHGGIY
          GVQILLYGDLPKNKENIIYLSNHQSTVDWIVADILAIRQN.LGHVRYVLKDGLKWLPLYGCYFSQHGGIY
Retrocopy GVQILLYGDLPKNKENIIYLSNHQSTVDWIVADILAIRQNVLGHVRYVLKDGLKWLPLYGCYFSQHGGIY

Parental  VKRSA-KFNEKEMRNKLQSHMKAGTPMFLVIFPEGTRYNPELTKVISASQTFAAQE
          VKRSA..FNEKEMRNKLQSHMKAGTPMFLVIFPEGTRYNPELTKVISASQTFAAQE
Retrocopy VKRSA<QFNEKEMRNKLQSHMKAGTPMFLVIFPEGTRYNPELTKVISASQTFAAQE

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	22.75 RPM	22.36 RPM
SRP012922_cerebellum	4.40 RPM	6.74 RPM
SRP012922_heart	1.62 RPM	2.78 RPM
SRP012922_kidney	4.11 RPM	4.93 RPM
SRP012922_liver	3.56 RPM	4.80 RPM
SRP012922_lung	5.35 RPM	5.19 RPM
SRP012922_quadricep_muscle	1.38 RPM	3.12 RPM
SRP012922_spleen	7.33 RPM	10.07 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_823 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005142	1 retrocopy	retro_chof_376,
Dasypus novemcinctus	ENSDNOG00000004979	1 retrocopy	retro_dnov_823 ,
Dipodomys ordii	ENSDORG00000008708	1 retrocopy	retro_dord_523,
Otolemur garnettii	ENSOGAG00000008958	1 retrocopy	retro_ogar_3477,
Ochotona princeps	ENSOPRG00000014343	3 retrocopies	retro_opri_343, retro_opri_829, retro_opri_935,
Pongo abelii	ENSPPYG00000018320	1 retrocopy	retro_pabe_3671,
Sarcophilus harrisii	ENSSHAG00000000051	1 retrocopy	retro_shar_687,
Tupaia belangeri	ENSTBEG00000013084	1 retrocopy	retro_tbel_2948,