RetrogeneDB ID: retro_dnov_1857

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_33688:39260..39946(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDZK1
• Ensembl ID: ENSDNOG00000000375
• Aliases: None
• Description: PDZ domain containing 1 [Source:HGNC Symbol;Acc:8821]

Sequence

>retro_dnov_1857
GCCTCCACTTTCAAGCCCTAAGTATGTAAGCTGTCCAAACAAGAAGGGCAAAGGTATGGTTTCTTCCTGAGAATCAAGAA
GGACACTATTGGCCACCTGGTCCAGACGGTTGAGAAGGGCAGCCCGGCAGACAAGGCTGGTCTCCAGGATGGAGACAGAG
TTCTTAGGATCAATCATGTCTTTGTGGACAAGGAAGAGCATGTGCAGGTTGTGGATCTGGTCAGAAAGAGCAGACAGTCA
GTAACTAATCTGGTTCTGTATGGCAATTCCTTTGAGAAAGCTGCTAAAAAACAGGTCGACTTGAAGGCATTGCATCAGAG
TCAGAAGTCACGGGTTTGAGTGATGAGGAACTGCCCCCAGTGATGAATGGTGGAGTGGAGACTTGGACCCAGCCTTGCCT
GTGCCACCTGGTGAAGGAGGGGAGCAGCTATGGCTTCTCTCTGAAAACTGTCCATGGTCAAAAGCAGTAGATGACTGATA
TGATACCTCCAGGTGTGGCTATGACAGCTGGTATCCTAGCTGATGATCACTTGATTGAAGCGAATGGAGAGAAGGGAGAA
AATGCCAGCCATGAGGAAGTGGTTGAAAAGGTGAAGAAGTCAGGAAGCCATGTCACGTTTCTGCTGGTGGGTAAGGAAAC
AGATAAGCGCCACAGTGAGCAACAGATAAAATTCGAGAGAAACAGC

Alignment

ORF - retro_dnov_1857 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.79 %
• Parental protein coverage: 87.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASTFKPRACKLSKQEGQTYAFFLRIEKHTAGHLVRMVEKRSPAEKAGLQDGDRVLSINAVFVDNEEHMQV
          ASTFKP..CKLSKQEGQ.Y.FFLRI.K.T.GHLV..VEK.SPA.KAGLQDGDRVL.IN.VFVD.EEH.QV
Retrocopy ASTFKP*VCKLSKQEGQRYGFFLRIKKDTIGHLVQTVEKGSPADKAGLQDGDRVLRINHVFVDKEEHVQV

Parental  VDLVRKSGHSVTFLVLDGDSYEKAIKNQVDLKELGQSQK-VPGLSDEELPPVMNGGVETWTQPRLCYLVK
          VDLVRKS..SVT.LVL.G.S.EKA.K.QVDLK.L.QSQK.V.GLSDEELPPVMNGGVETWTQP.LC.LVK
Retrocopy VDLVRKSRQSVTNLVLYGNSFEKAAKKQVDLKALHQSQK<VTGLSDEELPPVMNGGVETWTQPCLCHLVK

Parental  EGNSYGFSLKTVHGKKGVYMTDILPQGVAMKAGILADDHLIEVNGENVEDASHEEVVEKVKKSGSHVMFL
          EG.SYGFSLKTVHG.K...MTD..P.GVAM.AGILADDHLIE.NGE..E.ASHEEVVEKVKKSGSHV.FL
Retrocopy EGSSYGFSLKTVHGQK-Q*MTDMIPPGVAMTAGILADDHLIEANGEKGENASHEEVVEKVKKSGSHVTFL

Parental  LVDKETDKHHSEQKIKFKRET
          LV.KETDK.HSEQ.IKF.R..
Retrocopy LVGKETDKRHSEQQIKFERNS

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	8.36 RPM
SRP012922_cerebellum	0.00 RPM	1.65 RPM
SRP012922_heart	0.00 RPM	0.23 RPM
SRP012922_kidney	0.00 RPM	282.01 RPM
SRP012922_liver	0.00 RPM	25.85 RPM
SRP012922_lung	0.00 RPM	1.22 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.17 RPM
SRP012922_spleen	0.00 RPM	0.80 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_1857 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011153	1 retrocopy	retro_cfam_298,
Dasypus novemcinctus	ENSDNOG00000000375	2 retrocopies	retro_dnov_1158, retro_dnov_1857 ,
Myotis lucifugus	ENSMLUG00000028785	1 retrocopy	retro_mluc_1116,
Oryctolagus cuniculus	ENSOCUG00000024935	1 retrocopy	retro_ocun_133,