RetrogeneDB ID: retro_dnov_332

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3711:233530..234939(+)
• Located in intron of: ENSDNOG00000000693

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000007803
• Aliases: None
• Description: None

Sequence

>retro_dnov_332
ATGTCGTCAGATGACAGAGAAGCTAAGGAGGATGAATTGCTGGCCTTGGCAAGCATTTATGATGGAGATGAATTTAGAAA
GGCAGAGTCCATCCAGGGTGGAGAAACCAGGATCTATCTGGATTTGCCACAAAATTTCAAGATATTTGTGAGCGGCAACT
CAGATGAGTGTCTCCAGAATAGTGGTTTTGAATACACCATTTGCTTTTGCCTCCACTTGTGCTGAACTTTGAACTGCCAC
CAGATTATCCATCCTCCTCCTCACCTTCATTCACACTTAGTGGCAAATGGCTGTCACAACTCAGCTATCTGCTCTGTGCA
AGCACTTAGACAATCTGTGGGAAGAACACCATGGCAAGTGGTCCTGTTTGCCTGGATACAGTTTCTTAAGGAAGAGATGT
TAGCTTACCTGAATACTGTCTCCCCTTTTGAGCTCAAGATGGGTTCTCAGGGAAAAGTGCAAAGGAGGACAGCTCAAGCA
ACTCTCAACAAGAGCTAGATTTTGGAGGTGGTGCTGCTGGATCTGATGTAGACCAAGAGGAAGTGGTGGACAAAAGAGCT
GTACAGGACATGGAGTCACTGTAGAGTCTGATCCAGGAAATCTTGGACTTTGATCAAGCTCAGCAGAAAAAATGTTTTAA
CAGTAAATTGTTCCTGTGCAATAATTGTTTCTGTGAGAAGCTAGGTAGTGAATACATGTACTTCTTAGAGTGCAGGCATG
TATACTGCAAAGCCTTTCTGAAGGACTACTTTAAAATCCAGATCAAAGATGGCAAAGTTCATTGCCTCAACTGCCCAGAA
CCAAAGTGCCCTTCGGTGGCCACCCCTGGTCAGGTCAAAGGGCTAGTGGAAGCAGAGCTATTTGCTCGTTATGACCACCT
TCTCCTCCAGTCCACCTTGGACCTGATGGCAGATGTGGTGTACTGCCCCCACCCATGCCACCAACTGCCTGTGATGCAGG
AGCCAGGCTGCACCATGGGCCTCTGCTCCAGCTGCAATTTTGCCTTCTGCACCTTGTGCAGACTGACCTACCGTGGAGTC
TCTCTGTGTAAGTTCACCACAGAGAAGTTAATGGACTTACGAAATGAATACTTGCAAGCAGATGAGGCCAATAAGAGATT
TTTGGAACAGAGGTATGATAAGAGGGTGATTCAGAAGGTACTTGAAGAGATGGAAAGTAAGGAGTGACTAGAAAGGAACT
CAAATAGCTGCCCGTGTTGTGGGACTCCCATAGAGAAATGGGATGTAACAAGATGACATGTACTGGCTGCATGCAGTTTA
TCTGCTGGATTTGCATGGGTTCTCTCTCTAGAGCAAACAAACCCTTATCAACATTTCACTGATCCTTCTTCTCCTAGTTT
GAACCAGTTGTTCCGTGATGTAGATGTTAATGGAGACATTTGGGAAGAT

Alignment

ORF - retro_dnov_332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.16 %
• Parental protein coverage: 99.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSSEDREAQEDELLALASIFDGDEFKKAESIQGGESRIYLHLPQNFKIFVSGNSNESLQNSGFEHTVCF-
          MSS.DREA.EDELLALASI.DGDEF.KAESIQGGE.RIYL.LPQNFKIFVSGNS.E.LQNSGFE.T.CF.
Retrocopy MSSDDREAKEDELLALASIYDGDEFRKAESIQGGETRIYLDLPQNFKIFVSGNSDECLQNSGFEYTICF<

Parental  LPPLVLNFELPPDYPSSSPPSFTLSGKWLSP-TQLSALCEHLDSLWEEHRGT-VVLFAWMQFLKEETLAY
          LPPLVLNFELPPDYPSSS.PSFTLSGKWLS..TQLSALC.HLD.LWEEH.G..VVLFAW.QFLKEE.LAY
Retrocopy LPPLVLNFELPPDYPSSSSPSFTLSGKWLSQ<TQLSALCKHLDNLWEEHHGK<VVLFAWIQFLKEEMLAY

Parental  LNIVSPFELKMGSQGKVQRRPAQASLNT-ELDFAGGAAGSDVDQEEVVDERAVQDVESLSSLIQEILDFD
          LN.VSPFELKMGSQGKVQRR.AQA.LN..ELDF.GGAAGSDVDQEEVVD.RAVQD.ESL.SLIQEILDFD
Retrocopy LNTVSPFELKMGSQGKVQRRTAQATLNK<ELDFGGGAAGSDVDQEEVVDKRAVQDMESL*SLIQEILDFD

Parental  QAQQKKCFNSKLFLCNICFCEKLGSACMYFLECRHVYCKACLKDYFEIQIKDGQVHCLNCPEPKCPSVAT
          QAQQKKCFNSKLFLCN.CFCEKLGS..MYFLECRHVYCKA.LKDYF.IQIKDG.VHCLNCPEPKCPSVAT
Retrocopy QAQQKKCFNSKLFLCNNCFCEKLGSEYMYFLECRHVYCKAFLKDYFKIQIKDGKVHCLNCPEPKCPSVAT

Parental  PGQVKELVEAELFARYDRLLLQYTLDLMADVVYCPRPCCQLPVMQEPGETMGICSSCSFAFCTLCRLTYH
          PGQVK.LVEAELFARYD.LLLQ.TLDLMADVVYCP.PC.QLPVMQEPG.TMG.CSSC.FAFCTLCRLTY.
Retrocopy PGQVKGLVEAELFARYDHLLLQSTLDLMADVVYCPHPCHQLPVMQEPGCTMGLCSSCNFAFCTLCRLTYR

Parental  GVSPCNVTSGKLMELGKEYLKADEANKRFLEQRYGKKIIQKALEEMKSKKWLKKNSKSCPCCGTPIEKLD
          GVS.C..T..KLM.L..EYL.ADEANKRFLEQRY.K..IQK.LEEM.SK..L..NS.SCPCCGTPIEK.D
Retrocopy GVSLCKFTTEKLMDLRNEYLQADEANKRFLEQRYDKRVIQKVLEEMESKE*LERNSNSCPCCGTPIEKWD

Parental  GCNKMTCTACKQYFCWICLRSLSRAKPYKHFTDPSSPCXXXLFHGIHVNGDIEDE
          ........AC..........SL....PY.HFTDPSSP....LF....VNGDI...
Retrocopy VTR*HVLAACSLSAGFAWVLSLEQTNPYQHFTDPSSPSLNQLFRDVDVNGDIWED

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	2.33 RPM	1.17 RPM
SRP012922_cerebellum	1.51 RPM	1.10 RPM
SRP012922_heart	2.09 RPM	0.93 RPM
SRP012922_kidney	2.19 RPM	0.82 RPM
SRP012922_liver	0.93 RPM	1.24 RPM
SRP012922_lung	1.22 RPM	0.61 RPM
SRP012922_quadricep_muscle	2.42 RPM	3.12 RPM
SRP012922_spleen	1.60 RPM	1.49 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_332 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
Dasypus novemcinctus	ENSDNOG00000007803	1 retrocopy	retro_dnov_332 ,
Dasypus novemcinctus	ENSDNOG00000024423	1 retrocopy	retro_dnov_1704,
Homo sapiens	ENSG00000013561	2 retrocopies	retro_hsap_3790, retro_hsap_3881,
Gorilla gorilla	ENSGGOG00000008542	1 retrocopy	retro_ggor_2612,
Macaca mulatta	ENSMMUG00000009768	2 retrocopies	retro_mmul_1647, retro_mmul_934,
Oryctolagus cuniculus	ENSOCUG00000016953	1 retrocopy	retro_ocun_340,
Pongo abelii	ENSPPYG00000015894	2 retrocopies	retro_pabe_3095, retro_pabe_3115,
Pan troglodytes	ENSPTRG00000017356	2 retrocopies	retro_ptro_2571, retro_ptro_2643,