RetrogeneDB ID: retro_dnov_2677

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_9746:42503..43298(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPS1L1
• Ensembl ID: ENSDNOG00000002028
• Aliases: None
• Description: phosphoribosyl pyrophosphate synthetase 1-like 1 [Source:HGNC Symbol;Acc:9463]

Sequence

>retro_dnov_2677
GAGAGTGTATGTGGAGAAGGTATCTACATTGTTCAGAATGGTCATGGTGAAATCAAGGTCAATCTCATTGAAGTTTTGAT
TATGATTAATGCTTACAAGATCGCTTCAGCCAGCTGGGTTACCATAGCCATCCGTGCTTCCCTTAGCCTGGCAGGATAAG
AAGAATAAGAGCCAGGGCCCAATCTTGGCCAAGCTTGTCACAAATATGCTATATGTAGCAGCACAGATCATATTATCACC
ATGGATCTACATGCTTCTCAAATTCAGGGCTTTTTTGATATTTTATATGCAGAGCCAGCTGTCCTGAAGTGGACAAAGGA
GAACATCTCTGAATGGAGAAACTGTACCATTGTCTTCTGGGATGCTGGTAGAGCTAAGAGAGTGACCTCCACTGTAGACC
GATTGAATGTGGACTTTGCCTTGGTGTTCAAAGTATGGAAGAAAGCCAGAGAAGTGGGACATATGGTGCTGGTGGGAGAT
GTGAAGGATGGAGTGACTATCTTTGTAGATGACATGACTGATACTTGTGGTACAATCTGTCATTCAGCTGACAACTTCTC
TCACCTGGAGCCACCAGAGTTTATGCTATCTTGACTCATGGAATCTTTTCTGCCCTGGCCATTTCTCACATCAACAATGA
GTGTTTTGAAGCAATAGTGGTCACCAATAGCATACCTCAAGAGGATAAGATGAAGCGTTGCTTCAAAGTCCAGGTGATCG
ATATCTCCATGATCCTTGCAGAAGCCATCAGGAGAACTCACAAGGGGGAAATCCGTTTCCTACCTGTTCAGCCAT

Alignment

ORF - retro_dnov_2677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.73 %
• Parental protein coverage: 84.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ESVRGEDVYIVQSGCSEINDNLMELLIMINACKIASASRVTAVI-PCFP-YARQDKKDKSRAPISAKLVA
          ESV.GE..YIVQ.G..EI..NL.E.LIMINA.KIASAS.VT..I.PCFP..A.QDKK.KS..PI.AKLV.
Retrocopy ESVCGEGIYIVQNGHGEIKVNLIEVLIMINAYKIASASWVTIAI<PCFP<LAWQDKKNKSQGPILAKLVT

Parental  NMLSVAG-ADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIKENISE-RNCTIVSPDAGGAKRVTSIA
          NML.VA...DHIITMDLHASQIQGFFDI....LYAEPAVLKW.KENISE.RNCTIV..DAG.AKRVTS..
Retrocopy NMLYVAA<TDHIITMDLHASQIQGFFDI----LYAEPAVLKWTKENISEWRNCTIVFWDAGRAKRVTSTV

Parental  DRLNVDFALIHKERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAAD-KLLSAGATRVYAILTHG
          DRLNVDFAL..K..KKA.EV..MVLVGDVKD.V.I.VDDM.DTCGTICH.AD..LLS.GATRVYAILTHG
Retrocopy DRLNVDFALVFKVWKKAREVGHMVLVGDVKDGVTIFVDDMTDTCGTICHSAD<QLLSPGATRVYAILTHG

Parental  IFSGPAISRINNACFEAVVVTNTIPQEDKMKHCSKIQVIDISMILAEAIRRTHNGE-SVSYLFSH
          IFS..AIS.INN.CFEA.VVTN.IPQEDKMK.C.K.QVIDISMILAEAIRRTH.GE.SVSYLFSH
Retrocopy IFSALAISHINNECFEAIVVTNSIPQEDKMKRCFKVQVIDISMILAEAIRRTHKGE>SVSYLFSH

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	15.56 RPM
SRP012922_cerebellum	0.00 RPM	38.08 RPM
SRP012922_heart	0.00 RPM	10.91 RPM
SRP012922_kidney	0.00 RPM	15.88 RPM
SRP012922_liver	0.00 RPM	17.18 RPM
SRP012922_lung	0.00 RPM	30.85 RPM
SRP012922_quadricep_muscle	0.00 RPM	27.00 RPM
SRP012922_spleen	0.00 RPM	37.31 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_2677 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002028	2 retrocopies	retro_dnov_2677 , retro_dnov_947,
Dasypus novemcinctus	ENSDNOG00000003550	1 retrocopy	retro_dnov_280,
Dipodomys ordii	ENSDORG00000014534	2 retrocopies	retro_dord_356, retro_dord_632,
Echinops telfairi	ENSETEG00000014736	1 retrocopy	retro_etel_267,
Macropus eugenii	ENSMEUG00000010071	2 retrocopies	retro_meug_1612, retro_meug_443,
Oryctolagus cuniculus	ENSOCUG00000012391	3 retrocopies	retro_ocun_430, retro_ocun_867, retro_ocun_912,
Ochotona princeps	ENSOPRG00000013140	1 retrocopy	retro_opri_704,