RetrogeneDB ID: retro_dnov_371

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4157:82461..83307(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000005766
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: THRB
• Ensembl ID: ENSDNOG00000008172
• Aliases: None
• Description: thyroid hormone receptor, beta [Source:HGNC Symbol;Acc:11799]

Sequence

>retro_dnov_371
AGTTGCCTGGACAAAGAAGAGCAGTGTGTTGTGTGTGGGGACAAGGCAACCGGTTACCACTACCGCTGCCTCACTTGTGA
GGGTTGTGAGGGCTTCTTTCGCCGCACGATCCAGAAAAACCGCCAGCCCACCTACTCCTGCAAATATGACAGCTGCTGTG
TCATCGACAAGATCACCCGCAATCAGTGCCAACTGTGCCGCTTCAACAAGTGCATCGCCGCGGGCATGGTCATGGACTTA
GTTGTAGATGACTCCAAGCCGGTGGCTAAGCGCAAGCTGACGAAACAGAACCGGGAGCGGCAGCGAAAGAAGAAGAGCCC
ATCACTGCAGCCGCGACCAGAGCCTACCCCGGAGGAGTGGGATCTGATCCACATTGCGACGGAAGCCCATCGCAGCACCA
GTTCCCAGGGCAGCTGTTGGAAGCAGAGGAGGAAATTCCTGCAAGATGACATTGGCCAGTCACCCATCGTTTCCTTGCCA
GACGGCGACAAGGTCGACCTAGAGGCCTTCAGCGAATTTACCAAGGTCATCACCCCCGCCATCACCCGCGTGGTGGACTT
TGCCAAAAAACTGCCCATGTTCTCTGAGCTGCCTTGCGAAGACCAGATCATCCTCCTGAAGGGATGCTGCATGGAGATTA
TGTCCCTGCGGGCGGCTGCCCGCTATGACCCCGAGAGCGACACCCTCACACTGAGTGGAGAGGTGGCAGTCAAGCGGGAG
CAGCTCCAGCATGGCGGTCTGGGCGAAGTCTCCGACGCCATCTTTGAACTGGGCAAGTCACTCTCTGCCTTTAACCTGGA
TGACACGGAAGTGGCTCTGCTACAAGCTGTGCTGCTCTTGTCAACA

Alignment

ORF - retro_dnov_371 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.91 %
• Parental protein coverage: 71.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SYLDKDELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKK
          S.LDK.E.CVVCGDKATGYHYRC.TCEGC.GFFRRTIQKN..P.YSCKY...CVIDK.TRNQCQ.CRF.K
Retrocopy SCLDKEEQCVVCGDKATGYHYRCLTCEGCEGFFRRTIQKNRQPTYSCKYDSCCVIDKITRNQCQLCRFNK

Parental  CIYVGMATDLVLDDSKRLAKRKLIEENREKRRREELQKSIGHKPEPTDEEWELIKTVTEAHVATNAQGSH
          CI..GM..DLV.DDSK..AKRKL...NRE..R......S....PEPT.EEW.LI...TEAH..T..QGS.
Retrocopy CIAAGMVMDLVVDDSKPVAKRKLTKQNRERQRKKK-SPSLQPRPEPTPEEWDLIHIATEAHRSTSSQGSC

Parental  WKQKRKFLPEDIGQAPIVNAPEGGKVDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGC
          WKQ.RKFL..DIGQ.PIV..P.G.KVDLEAFS.FTK.ITPAITRVVDFAKKLPMF.ELPCEDQIILLKGC
Retrocopy WKQRRKFLQDDIGQSPIVSLPDGDKVDLEAFSEFTKVITPAITRVVDFAKKLPMFSELPCEDQIILLKGC

Parental  CMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLL
          CMEIMSLRAA.RYDPES.TLTL.GE.AV.R.QL..GGLG.VSDAIF.LG.SLS.FNLDDTEVALLQAVLL
Retrocopy CMEIMSLRAAARYDPESDTLTLSGEVAVKREQLQHGGLGEVSDAIFELGKSLSAFNLDDTEVALLQAVLL

Parental  MSS
          .S.
Retrocopy LST

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	25.86 RPM	9.92 RPM
SRP012922_cerebellum	57.05 RPM	1.37 RPM
SRP012922_heart	12.99 RPM	3.94 RPM
SRP012922_kidney	24.37 RPM	3.56 RPM
SRP012922_liver	11.30 RPM	5.73 RPM
SRP012922_lung	45.82 RPM	3.82 RPM
SRP012922_quadricep_muscle	17.83 RPM	7.10 RPM
SRP012922_spleen	48.30 RPM	8.70 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_371 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008172	1 retrocopy	retro_dnov_371 ,