RetrogeneDB ID: retro_dnov_2262

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_59744:8105..8811(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TARDBP
• Ensembl ID: ENSDNOG00000008531
• Aliases: None
• Description: TAR DNA binding protein [Source:HGNC Symbol;Acc:11571]

Sequence

>retro_dnov_2262
GTTATGGCCCAGTTTCCAGGGGCATGTGGTATATGCTACAGGAATCCAGTGTTTCAGTGTATGAGAGGTGTCCACCTAGT
AGAAGGAACTCTGCATATACCTAATGCCAACTGGGGAAATCTGGCGTATGTTGTCAACTATCCCAAAGATAATGATAACA
ACAACAAAAATGGATGAAACTGATGCTTCATCAGCAGTGAAAGTGAAAAAAGCATCTGATTTAATAGTGTTGGGCTTTCA
ATGGAAAACAACTGAACAGGATCTAAAAGAATATATTAGTACCTTTGGAGAAGTTCTTATGGTGCAGGTCAGGAAAGATA
TTCAAACTGGTCATTCAAAAGGGTTTGGCTTTGTTTGTTTTATGGAATATGAAACCGAGGTGGAAATAATATCACAGCAA
CATATGATAGATGGGCAGTTGTCTGACTGTAAACTTCTTAGTTCTAAGCAAAGCCCAGATGAGCTTTTGAGAAGCAGGAA
GATGTTCATTGGGCATTGTACAGAGGACAGGACTGCTGCTTATTTGCTGCAGTTCTTTTGCAAGTATAGAGAAGTGGTAG
ACATCTTTATTCCCAAACCATTGAAGATTTTTGCTTTCATTACATTTGCAGATGAACAGGATGCCCAGTCTCTTTGCGGC
TAGTACTTGATCATTGAAGGAATCAGTGTATGTATATCCAACAATGAACCTAAGCACAACAGGAAT

Alignment

ORF - retro_dnov_2262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 57.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTAQFPGACGLRYRNPVSQCMRGVRLVEGVLHAPDAGWGNLVYVVNYPK--DNKRK-MDETDASSAVKVK
          V.AQFPGACG..YRNPV.QCMRGV.LVEG.LH.P.A.WGNL.YVVNYPK..DN..K.MDETDASSAVKVK
Retrocopy VMAQFPGACGICYRNPVFQCMRGVHLVEGTLHIPNANWGNLAYVVNYPKDNDNNNK>MDETDASSAVKVK

Parental  RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDIKTGHSKGFGFVRFTEYETQVKVMSQRHM
          .A....SDLIVLG..WKTTEQDLKEY.STFGEVLMVQV.KDI.TGHSKGFGFV.F.EYET.V...SQ.HM
Retrocopy KA----SDLIVLGFQWKTTEQDLKEYISTFGEVLMVQVRKDIQTGHSKGFGFVCFMEYETEVEIISQQHM

Parental  IDGRWCDCKLPNSKQSPDEPLRSRKVFVGRCTEDMTADELQQFFCQYGEVVDVFIPKPFRAFAFVTFADD
          IDG...DCKL..SKQSPDE.LRSRK.F.G.CTED.TA..L.QFFC.Y.EVVD.FIPKP...FAF.TFAD.
Retrocopy IDGQLSDCKLLSSKQSPDELLRSRKMFIGHCTEDRTAAYLLQFFCKYREVVDIFIPKPLKIFAFITFADE

Parental  QVAQSLCGEDLIIKGISVHISNAEPKHNSN
          Q.AQSLCG..LII.GISV.ISN.EPKHN.N
Retrocopy QDAQSLCG*YLIIEGISVCISNNEPKHNRN

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	70.79 RPM
SRP012922_cerebellum	0.00 RPM	83.31 RPM
SRP012922_heart	0.00 RPM	35.27 RPM
SRP012922_kidney	0.00 RPM	34.22 RPM
SRP012922_liver	0.00 RPM	31.27 RPM
SRP012922_lung	0.00 RPM	52.08 RPM
SRP012922_quadricep_muscle	0.00 RPM	35.14 RPM
SRP012922_spleen	0.00 RPM	72.11 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_2262 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002381	2 retrocopies	retro_cjac_2457, retro_cjac_525,
Dasypus novemcinctus	ENSDNOG00000008531	1 retrocopy	retro_dnov_2262 ,
Dasypus novemcinctus	ENSDNOG00000014501	1 retrocopy	retro_dnov_1423,
Homo sapiens	ENSG00000120948	2 retrocopies	retro_hsap_1209, retro_hsap_3637,
Macaca mulatta	ENSMMUG00000007456	1 retrocopy	retro_mmul_1847,
Mus musculus	ENSMUSG00000041459	1 retrocopy	retro_mmus_1958,
Nomascus leucogenys	ENSNLEG00000009512	2 retrocopies	retro_nleu_201, retro_nleu_819,
Pongo abelii	ENSPPYG00000001894	1 retrocopy	retro_pabe_1008,
Pan troglodytes	ENSPTRG00000000136	2 retrocopies	retro_ptro_2460, retro_ptro_828,
Sus scrofa	ENSSSCG00000023126	1 retrocopy	retro_sscr_652,
Drosophila melanogaster	FBgn0025790	1 retrocopy	retro_dmel_17,