RetrogeneDB ID: retro_dnov_459

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4984:23033..24000(+)
• Located in intron of: ENSDNOG00000025775

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOP58
• Ensembl ID: ENSDNOG00000002285
• Aliases: None
• Description: NOP58 ribonucleoprotein [Source:HGNC Symbol;Acc:29926]

Sequence

>retro_dnov_459
CTTTCTCAATATGGGTTGAAATTTAGCGCTAATAAAGTAGACACAATAATTGTTCAAGCAATTTCCTTGTTAGACAACTT
TGATAAAGAACTAAATAACATACATTATGTAGTGTAGAGAATGGTATGGCTGGCATTTCCCTGAACTAGGAAAAATTATT
TCAGATAATTTGACATACTGCAAGTGTTTACAGAAAGTTGGCGACAGGAAGAACTATGCCTCTGCCAAACTTTCTGAATT
ACTGCCAGAAGATATTGAAGCAGAAGTGAAAGCAGCTGCAGAGATATCTATGGGAACAGAAGTTTCAGAAGAAGATATTT
GCAATATTCTACATCTCTGTACCCAGGTGACTGAAATCTCAGAATATAGAACCCAGCTCTATGAATATCTACAAAATTGA
ATGATGGCCATTGCACCTAATGTTACAGTCATGGTTGGGGAATTAGTTGGAGCATGGCTTATTGCTCATGCAAGTTCTCT
TTTTAATTTGGCCAAGCATGCCGTGTCTACAGTTCAGATTCTTGGAGCAGAAAAGGCACTCTTCAGAGCCCTCAAGTCAA
GACGGGATACCTGTAAGGATGGTCTCATTTATCATATTTCACTTGTAGGACAGACAAGTCCCAAACACAAAGGAAAGATT
TCTCGAATGCTGGCAGCCAAAACTGTTTTGGTCAACCATTATGATGCTTTTGATGAGGATTCTAGTTCTGCAGTGGGAGT
TGAGAAGTGATCCAAATTAGAGGCCAGGCTGAGGACCTTGGAAGACAGAGGGATAAGAAAAATAAGTGGAACAAGAAAGG
CATTAGCAAAAAACAGAAAAATATGAACATACAAGTGAAGTGAAGACTTATGACCTTTCTGGTGACTCTACACTGCCAAC
AATTTCTAAAAACGCAAGATAGACCAGGTAGATAAAGAGGAGGAAACTACTGAAAAGAAAGCCAAAAAAGCCAAGATTAA
AATCAAA

Alignment

ORF - retro_dnov_459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.46 %
• Parental protein coverage: 62.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSRYRLKFSADKVDTMIVQAISLLDDLDKELNN-YIMRCREWYGWHFPELGKIISDNLTYCKCLQKVGDR
          LS.Y.LKFSA.KVDT.IVQAISLLD..DKELNN.YIM.CREWYGWHFPELGKIISDNLTYCKCLQKVGDR
Retrocopy LSQYGLKFSANKVDTIIVQAISLLDNFDKELNN>YIM*CREWYGWHFPELGKIISDNLTYCKCLQKVGDR

Parental  KNYASAKLSELLPEDIEAEVKAAAEISMGTEVSEEDICNILHLCTQVIEISEYRTQLYEYLQNRMMAIAP
          KNYASAKLSELLPEDIEAEVKAAAEISMGTEVSEEDICNILHLCTQV.EISEYRTQLYEYLQN.MMAIAP
Retrocopy KNYASAKLSELLPEDIEAEVKAAAEISMGTEVSEEDICNILHLCTQVTEISEYRTQLYEYLQN*MMAIAP

Parental  NVTVMVGELVGARLIAHAGSLLNLAKHAASTVQILGAEKALFRALKSRRDTPKYGLIYHASLVGQTSPKH
          NVTVMVGELVGA.LIAHA.SL.NLAKHA.STVQILGAEKALFRALKSRRDT.K.GLIYH.SLVGQTSPKH
Retrocopy NVTVMVGELVGAWLIAHASSLFNLAKHAVSTVQILGAEKALFRALKSRRDTCKDGLIYHISLVGQTSPKH

Parental  KGKISRMLAAKTVLAIRYDAFGEDSSSAMGVENRAKLEARLRTLEDRGIRKISGTGKALA-KTEKYEHKS
          KGKISRMLAAKTVL...YDAF.EDSSSA.GVE...KLEARLRTLEDRGIRKISGT.KALA.KTEKYEH.S
Retrocopy KGKISRMLAAKTVLVNHYDAFDEDSSSAVGVEK*SKLEARLRTLEDRGIRKISGTRKALA>KTEKYEHTS

Parental  EVKTYDPSGDSTLPTCSK-KRKIDQVDKEEETTEKKAKKAKIKIK
          EVKTYD.SGDSTLPT.SK.KRKIDQVDKEEETTEKKAKKAKIKIK
Retrocopy EVKTYDLSGDSTLPTISK<KRKIDQVDKEEETTEKKAKKAKIKIK

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	0.39 RPM	31.31 RPM
SRP012922_cerebellum	0.82 RPM	26.12 RPM
SRP012922_heart	0.00 RPM	12.53 RPM
SRP012922_kidney	0.27 RPM	19.99 RPM
SRP012922_liver	0.15 RPM	18.27 RPM
SRP012922_lung	0.92 RPM	45.36 RPM
SRP012922_quadricep_muscle	0.00 RPM	9.87 RPM
SRP012922_spleen	1.37 RPM	43.95 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_459 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002285	1 retrocopy	retro_dnov_459 ,