RetrogeneDB ID: retro_dnov_40

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2565:48196..49183(+)
• Located in intron of: ENSDNOG00000013756

Retrocopy information

• Ensembl ID: ENSDNOG00000013766
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DNAJA2
• Ensembl ID: ENSDNOG00000013794
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 2 [Source:HGNC Symbol;Acc:14884]

Sequence

>retro_dnov_40
GATGATATTTTCTCTCACATTTTTGGTGGGGGATTGTTTGGCTTCATGGGCAATCAGAGTAGAAGTCAAAATGGCAGAAG
AAGAGGAGAAGACATGATGCATTCCATCAAAGTATCTTTTGAAGATTTGTATAATGGCAAGACAACCAAACTACAACTTA
GCAAGAATGTACTCTGTAGTGCATGCAGTGGCCAAGGCGGAAAGCCTGGAGCTGTTCAGAAGTGTAGCGCTTGTCGAGGT
CGAGGTGTACGCATCATGATCAGACAGCTGGCTCCAGGCATGGTGCAACAGATGCAGTCTGTGTGCTCTGATTGTAATGG
AGAAGGAGAGGTAATTAATGGAAAAGACCGCTGTAAAAAATGTGAGGGCAAGAAAGTGATTAAAGAAGTCAAGATTCTTG
AAGTCCACGTAGACAAAGGCATGAAACATGGACAGAGAATTAAATTTACTGGGGAAGCAGACCAAGCCCCAGGAATGGAA
CCAGGAGACATTGTTCTTTTGCTACAAGAGAAAGAACATGAGGTGTTCCAGAGAGATGGAAATGATTTGCACAGGACGTA
TAAGATAGGACTTGTTGAAGCTCTGTGTGGATTTCAGTTCACATTTAAGCACCTTGATGGCTGTCAGATTGTGATGAAAT
ACCCCCCTGGCAAAGTAATTGAACCAGGATGTGTGCGTGTAGTTCGAGGTGAAGGAATGCCACTGTACCGGAATCCCTTT
GAAAAAGGTGATCTTTACATAAAGTTTGATGTACAGTTTCCTGAAAACAACTGGATTAACCCAGCCAAGCTTTCTGAACT
AGAAGATCTTCTGCCATCTAGACCGGAAGTTCCTAATGTCATTGGAGACACAAAGGAGGTAGAGCTTCAGGAGTTTGATA
GCACTCGGGGCTCGGGAGGTGGTCAGAGGCGCGAAGCCCGCAATGATAGCTCTGATGAGGAAAGCAGCAGCCATCACGGA
CCTGGAGTGCAGTGTGCCCATCAGTAA

Alignment

ORF - retro_dnov_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.09 %
• Parental protein coverage: 75.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDIFSHIFGGGLFGFMGNQSRSRNGRRRGEDMMHPLKVSLEDLYNGKTTKLQLSKNVLCSACSGQGGKSG
          DDIFSHIFGGGLFGFMGNQSRS.NGRRRGEDMMH..KVS.EDLYNGKTTKLQLSKNVLCSACSGQGGK.G
Retrocopy DDIFSHIFGGGLFGFMGNQSRSQNGRRRGEDMMHSIKVSFEDLYNGKTTKLQLSKNVLCSACSGQGGKPG

Parental  AVQKCSACRGRGVRIMIRQLAPGMVQQMQSVCSDCNGEGEVINEKDRCKKCEGKKVIKEVKILEVHVDKG
          AVQKCSACRGRGVRIMIRQLAPGMVQQMQSVCSDCNGEGEVIN.KDRCKKCEGKKVIKEVKILEVHVDKG
Retrocopy AVQKCSACRGRGVRIMIRQLAPGMVQQMQSVCSDCNGEGEVINGKDRCKKCEGKKVIKEVKILEVHVDKG

Parental  MKHGQRITFTGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLHMTYKIGLVEALCGFQFTFKHLDGRQI
          MKHGQRI.FTGEADQAPG.EPGDIVLLLQEKEHEVFQRDGNDLH.TYKIGLVEALCGFQFTFKHLDG.QI
Retrocopy MKHGQRIKFTGEADQAPGMEPGDIVLLLQEKEHEVFQRDGNDLHRTYKIGLVEALCGFQFTFKHLDGCQI

Parental  VVKYPPGKVIEPGCVRVVRGEGMPQYRNPFEKGDLYIKFDVQFPENNWINPDKLS
          V.KYPPGKVIEPGCVRVVRGEGMP.YRNPFEKGDLYIKFDVQFPENNWINP.KLS
Retrocopy VMKYPPGKVIEPGCVRVVRGEGMPLYRNPFEKGDLYIKFDVQFPENNWINPAKLS

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	12.06 RPM	36.17 RPM
SRP012922_cerebellum	12.51 RPM	40.28 RPM
SRP012922_heart	11.37 RPM	23.20 RPM
SRP012922_kidney	13.69 RPM	19.71 RPM
SRP012922_liver	9.91 RPM	28.02 RPM
SRP012922_lung	9.47 RPM	27.03 RPM
SRP012922_quadricep_muscle	19.56 RPM	40.33 RPM
SRP012922_spleen	11.68 RPM	30.90 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_40 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003757	3 retrocopies	retro_btau_1215, retro_btau_1625, retro_btau_798,
Cavia porcellus	ENSCPOG00000006955	1 retrocopy	retro_cpor_1466,
Dasypus novemcinctus	ENSDNOG00000013794	1 retrocopy	retro_dnov_40 ,
Dasypus novemcinctus	ENSDNOG00000018342	3 retrocopies	retro_dnov_1139, retro_dnov_640, retro_dnov_884,
Macaca mulatta	ENSMMUG00000002247	1 retrocopy	retro_mmul_36,
Oryctolagus cuniculus	ENSOCUG00000004839	1 retrocopy	retro_ocun_1126,
Rattus norvegicus	ENSRNOG00000016251	1 retrocopy	retro_rnor_2778,
Ictidomys tridecemlineatus	ENSSTOG00000004007	1 retrocopy	retro_itri_343,