RetrogeneDB ID: retro_dnov_1663

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_2589:78500..79516(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDX
• Ensembl ID: ENSDNOG00000019413
• Aliases: None
• Description: radixin [Source:HGNC Symbol;Acc:9944]

Sequence

>retro_dnov_1663
GAAATAAAAAATAAATAGGGAATTGAATTGTTGTTAAGCATTGACGCTTTGGGTCTGAATATTTATGAGCATGATAACAG
GGTAACATCTAAAATTGATTTTCCCTGGAGTGAAATCAGAAATACTTCATTTAATGACCAAAAAAAAAAAATTGTTATAA
AACCATTTGACAAAAGGCACCTGATTTTGTTTTTTATGCAGCTTGTCTGAGAATAAGTGTATTTTGGCTTTATGTATGGG
AAGCCATGAGCTGTATATGCAAAGATGGAAGCTTAATACTTTTGAAGTACAACAGATGAAAGTTCAGGCTAGGGAAAAGT
TGTCAGAAGCAGTTGGAAAAGGGCACAGCTAGAGAATGAAACTGATAAGAAATAGCCGGAAAAGAAAAGGAAAGAATAGA
ACATGAAAAGGAAGAACTAATGGATCATCTAAGGCACATTGAAGAGCTGACAATGAAAATCCAGAAAGAACTAGAAAAAC
AGATTCACAAAGCTCTTGAGCTGGACTGGACTCAGAAATGAGCCAAAGAAGCAGAATGACTTGAAACGGAGCATTGAGCT
GCTTAAGAGGCCAAGTCTGCAATAGCAAAACAGGCTGCTGAAAAGATGAAGAATCAAGAACAGCTAGCAGCAGAACTTGC
CGAATTCACTGCCAAGACTGCACTTCTAGAAGAAGCCAAGAAGAAAAAGGCAGAGAAAGCTACTAAATGGCAAAACAAAG
CTTTTGCAACCCAGGAGGACTCGGAAAAGACCAAAAAAAGAGTTAAAAACCATGATGTCTGCCTTGCACACTCCACCGCT
GCTACCACTAGTCATTTCTCCAACAGAAAATGAGCATAATGAACATATTGAGAAGAGTAGGCAGGCAAGAGCTGAATTAT
CAAATGAAGGGGCGATGAAACATTGAAGTGAGGAAGAACATGTAACAGAAACACAGACAAATGAGCATATTAAGGAACAA
ATCCAGACATAAGTTCAAAATTTACCTGAGCCAAGGATGAAACCAAGAAAACAGAG

Alignment

ORF - retro_dnov_1663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.34 %
• Parental protein coverage: 56.29 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EIKNKKGTELWLGVDALGLNIYEHDDKLTPKIGFPWSEIRNISFNDKKF--VIKPIDK-KAPD-FVFYAP
          EIKNK.G.EL.L..DALGLNIYEHD...T.KI.FPWSEIRN.SFND.....VIKP.DK.KAPD.F.F...
Retrocopy EIKNK*GIELLLSIDALGLNIYEHDNRVTSKIDFPWSEIRNTSFNDXXXXXVIKPFDK<KAPD<FCFLCS

Parental  RLRINKRILALCMGNHELYMRRRKPDTIEVQQMKAQAREEKHQ-KQFGRAQLENEKKKREIAEKEK-ERI
          .L..NK.ILALCMG.HELYM.R.K..T.EVQQMK.QARE.........RAQLENE..K....EK...ERI
Retrocopy -LSENKCILALCMGSHELYMQRWKLNTFEVQQMKVQAREKLSE<SSWKRAQLENETDKK-*PEKKR<ERI

Parental  EREKEELMERLRQIEEQTMKAQKELEEQTRKALELDQERKRAKEEAERLEKERRAAEEAKSAIAKQAADQ
          E.EKEELM..LR.IEE.TMK.QKELE.Q..KALELD...K.AK.EAE.LE.E..AA.EAKSAIAKQAA..
Retrocopy EHEKEELMDHLRHIEELTMKIQKELEKQIHKALELDWTQK*AK-EAE*LETEH*AA*EAKSAIAKQAAEK

Parental  MKNQEQLAAELAEFTAKIALLEEAKKKKEEEATEWQHKAFAAQEDLEKT-KEELKTVMSA-PPPPPPPPV
          MKNQEQLAAELAEFTAK.ALLEEAKKKK.E.AT.WQ.KAFA.QED.EKT.K.ELKT.MSA...PP..P.V
Retrocopy MKNQEQLAAELAEFTAKTALLEEAKKKKAEKATKWQNKAFATQEDSEKT>KKELKTMMSALHTPPLLPLV

Parental  IPPTENEHDEHDENNAQASAELSNEGVMNHRSEEERVTETQKNERVKKQLQA-LSSELAQARDETKKTQ
          I.PTENEH.EH.E...QA.AELSNEG.M.H.SEEE.VTETQ.NE..K.Q.Q...SS....A.DETKKT.
Retrocopy ISPTENEHNEHIEKSRQARAELSNEGAMKH*SEEEHVTETQTNEHIKEQIQT<ISSKFT*AKDETKKTE

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	46.67 RPM
SRP012922_cerebellum	0.00 RPM	83.03 RPM
SRP012922_heart	0.00 RPM	76.80 RPM
SRP012922_kidney	0.00 RPM	173.86 RPM
SRP012922_liver	0.00 RPM	54.80 RPM
SRP012922_lung	0.00 RPM	337.67 RPM
SRP012922_quadricep_muscle	0.00 RPM	110.43 RPM
SRP012922_spleen	0.00 RPM	162.88 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_1663 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000019413	1 retrocopy	retro_dnov_1663 ,
Homo sapiens	ENSG00000137710	1 retrocopy	retro_hsap_840,
Gorilla gorilla	ENSGGOG00000027218	1 retrocopy	retro_ggor_689,
Pan troglodytes	ENSPTRG00000004259	1 retrocopy	retro_ptro_2281,