RetrogeneDB ID: retro_dnov_1863

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_34029:4014..5493(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADHA
• Ensembl ID: ENSDNOG00000006972
• Aliases: None
• Description: hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit [Source:HGNC Symbol;Acc:4801]

Sequence

>retro_dnov_1863
GTACCCCTGGGGATATTACCAGGAGCAGGAGGTACACAAAGGCTCCCCAAAATGGTGGGTATGCCTGCTGCTTTTGACAT
GATGCTGACTGGTAGAAATATTCGTGCAGACAGAGCAAAGAAAATGGGACTAGTTGACCAATTGGTGGAACCCTTGGGAC
CAGGAGTAAAACCTCCAGAGGAACGGACAATTGAATACCTAGAAGTTGCAGTGACTTTTGCCAAAGAACTGGCTGATAAA
AAGATTTCTCCCAAGAGAGACAAGGGATTGATGGAAAAACTGACGTCGTTTGCGATGACTATTCCATTTGTCAGGCAACA
AATTTACAAAAAGGTGGAAGAAAAAGTACGAAAGCAGACCAAAGGCCTTTATCCTGCACCACTGAAAATAATTGATGTGG
TAAAGACTGGAATTGAGCAAGGGATTGAGGCTGGCTATCTCTCTGAATCTCAGCAATTTGGAGACCTTGCAATGACCAAA
GAATCAAAGGCCTTGGTGGGACTTTACCATGGTCAGGTCCTGTGCAAGAAGAATAAATTTGGAGCACCTCAGAAGGATGT
TAAGCATCTAGCTATTCTTGGTGCAGGGCTGATGGGAGCCGGCATTGCCCAAGTCTCCGTGGATAAAGGGCTAAAGACTA
TACTTAAAGATGCTACAGTTGCCGGGCTAGGCAGAGGACAGCAACAAGTGTACAAAGGATTGAATGATAAAGTGAAGAAG
AAAGCTCTAACATCATTTGAAAGGGACTCCATTTTCAGCAACTTGACTGGGCAGCTCGATTACCAGGGTTTTGAAAAGGC
AGACATGGTGATTGAAGCTGTGTTTGAGGACCTTAGCCTCAAGCACAGAGTGCTAAAGGAAATCGAAGTGTTGATTCCAG
ATCACTGTGTCTTTGCCAGTAACACATCTGCTCTCCCAATCAGAGAAATTGCTGCTGTCAGCAAAAGACCTGAGAAGGTG
ATTGGCATGCACTACTTCTCTCCTGTGGACAAGATGCAGCTGCTGGAGATTATCACAACTGAAAAGACATCTAAGGACAC
AACTGCTTCTGCTGTAGCAGTTGGTCTCAAGCAGGGGAAGGTCATCATTGTGGTTAAGGATGGACCTGGCTTCTACACCA
CCAGGTGCCTTGCCCCCATGATGTCTGAAGTCATCCGGATTCTCCAGGAAGGAGTCGACCCCAAGAAACTGGATTCCCTG
ACCACAAGCTTTGGGTTTCCTGTGGGTGCTGCAACACTGGTGGATGAAGTTGGTGTGGATGTAGCTAAACATGTAGCCGA
AGATCTCGGCAAAGCCTTTGGGGAGCGGTTTGGAGGTGGAAGCATAGAACTGGTGCAGCAGATGGTATCCAAGGGCTTCC
TGGGTCGCAAGTCTGGGAAGGGCTTTTACGTCTACCAGGAGGGTGTGAAGAATAAGAATTTGAATTCTGACATGGATAGT
ATTTTGGCAAGTCTGAGGTTGACTCCTAAGTCTGATGTC

Alignment

ORF - retro_dnov_1863 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.55 %
• Parental protein coverage: 64.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLLGILPGAGGTQRLPKMVGMPAAFDMMLTGRNIRADRAKKMGLVDQLVEPLGPGVKPPEERTIEYLEEV
          V.LGILPGAGGTQRLPKMVGMPAAFDMMLTGRNIRADRAKKMGLVDQLVEPLGPGVKPPEERTIEYLE.V
Retrocopy VPLGILPGAGGTQRLPKMVGMPAAFDMMLTGRNIRADRAKKMGLVDQLVEPLGPGVKPPEERTIEYLE-V

Parental  AVTFAKELADKKISPKRDKGLMEKLTSFAMTIPFVRQQIYKKVEEKVRKQTKGLYPAPLKIIDXXXXXXX
          AVTFAKELADKKISPKRDKGLMEKLTSFAMTIPFVRQQIYKKVEEKVRKQTKGLYPAPLKIID.......
Retrocopy AVTFAKELADKKISPKRDKGLMEKLTSFAMTIPFVRQQIYKKVEEKVRKQTKGLYPAPLKIIDVVKTGIE

Parental  XXXXXXXXXXXXQFGDLAMTKESKALVGLYHGQVLCKKNKFGAPQKDVKHLAILGAGLMGAGIAQVSVDK
          ............QFGDLAMTKESKALVGLYHGQVLCKKNKFGAPQKDVKHLAILGAGLMGAGIAQVSVDK
Retrocopy QGIEAGYLSESQQFGDLAMTKESKALVGLYHGQVLCKKNKFGAPQKDVKHLAILGAGLMGAGIAQVSVDK

Parental  GLKTILKDATVAGLGRGQQQVYKGLNDKVKKKALTSFERDSIFSNLTGQLDYQGFEKADMVIEAVFEDLS
          GLKTILKDATVAGLGRGQQQVYKGLNDKVKKKALTSFERDSIFSNLTGQLDYQGFEKADMVIEAVFEDLS
Retrocopy GLKTILKDATVAGLGRGQQQVYKGLNDKVKKKALTSFERDSIFSNLTGQLDYQGFEKADMVIEAVFEDLS

Parental  LKHRVLKEVEVLIPDHCVFASNTSALPIREIAAVSKRPEKVIGMHYFSPVDKMQLLEIITTEKTSKDTTA
          LKHRVLKE.EVLIPDHCVFASNTSALPIREIAAVSKRPEKVIGMHYFSPVDKMQLLEIITTEKTSKDTTA
Retrocopy LKHRVLKEIEVLIPDHCVFASNTSALPIREIAAVSKRPEKVIGMHYFSPVDKMQLLEIITTEKTSKDTTA

Parental  SAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDSLTTSFGFPVGAATLVDEVGV
          SAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDSLTTSFGFPVGAATLVDEVGV
Retrocopy SAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDSLTTSFGFPVGAATLVDEVGV

Parental  DVAKHVAEDLGKAFGERFGGGSIELVQQMVSKGFLGRKSGKGFYVYQEGVKNKNLNSDMDSILASLRLTP
          DVAKHVAEDLGKAFGERFGGGSIELVQQMVSKGFLGRKSGKGFYVYQEGVKNKNLNSDMDSILASLRLTP
Retrocopy DVAKHVAEDLGKAFGERFGGGSIELVQQMVSKGFLGRKSGKGFYVYQEGVKNKNLNSDMDSILASLRLTP

Parental  KSDV
          KSDV
Retrocopy KSDV

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	57.76 RPM	149.55 RPM
SRP012922_cerebellum	18.15 RPM	65.85 RPM
SRP012922_heart	120.66 RPM	285.86 RPM
SRP012922_kidney	69.00 RPM	163.73 RPM
SRP012922_liver	59.76 RPM	161.77 RPM
SRP012922_lung	31.46 RPM	74.68 RPM
SRP012922_quadricep_muscle	152.83 RPM	412.11 RPM
SRP012922_spleen	38.80 RPM	97.29 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_1863 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006972	1 retrocopy	retro_dnov_1863 ,
Homo sapiens	ENSG00000084754	1 retrocopy	retro_hsap_958,
Gorilla gorilla	ENSGGOG00000004918	1 retrocopy	retro_ggor_772,
Macaca mulatta	ENSMMUG00000004380	2 retrocopies	retro_mmul_1987, retro_mmul_787,
Mustela putorius furo	ENSMPUG00000008546	1 retrocopy	retro_mputfur_705,
Nomascus leucogenys	ENSNLEG00000001616	2 retrocopies	retro_nleu_1588, retro_nleu_772,
Pongo abelii	ENSPPYG00000012583	2 retrocopies	retro_pabe_2576, retro_pabe_817,
Pan troglodytes	ENSPTRG00000011732	2 retrocopies	retro_ptro_2109, retro_ptro_664,
Ictidomys tridecemlineatus	ENSSTOG00000001593	1 retrocopy	retro_itri_681,