RetrogeneDB ID: retro_dnov_1090

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_145562:386..921(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDHB
• Ensembl ID: ENSDNOG00000006937
• Aliases: None
• Description: pyruvate dehydrogenase (lipoamide) beta [Source:HGNC Symbol;Acc:8808]

Sequence

>retro_dnov_1090
TTACAGGTCATCAGCCCCTGGAATTCAGAAGATGCAAAAGAACTTATTAAATTGGCCATTCGGATGACAATCAAATGGTG
GTGCTACAGCATGAACTGCTCTATGAATTTCCTGATGAAGCTCAGTAAAAGATTTTCTGATTCCTATTGGAAAAGCCAAA
AGGGACACATGTGACCATGGTGTCCCACTCAAGGCCTGTTGGCCCATGCTTAGAAGCTGCAACGGTGCTCTCTAACGAGG
GAGTTGAGTGAGAGGTGACAAACCTGCATACCATCAGACCGATGGACATCAAAGCTATAGAAGCCAATGTCATGAAGACA
CAGCATCTCGTAACTGTGGAAGGAGGCTGTCCACCATTTGGAGTAGATCTGAGATTTGTGTCAGGAACATACAATGTCCC
ATACTCAAATTCCTGGATACTCCTGCAGTTTGCATCGCTGGTGCTGATGTCCCTATGCCTCATGCAGAGATTCTGGGAGA
CAACTGCGCACCTCAGGTCAAAGACATCATATTTGCTGTAAAGAAAATACTAAAT

Alignment

ORF - retro_dnov_1090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.14 %
• Parental protein coverage: 52.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKVVSPWNSEDAKGLIKSAIR-DDNPVVMLENELMYGVPFEFPDEAQSKDFLVPIGKAKIERQGTHITVV
          L.V.SPWNSEDAK.LIK.AIR.DDN..V.L..EL......EFPDEAQ.K.F.....K.K....GTH.T.V
Retrocopy LQVISPWNSEDAKELIKLAIR<DDNQMVVLQHELL----YEFPDEAQ*KIF*FLLEKPK----GTHVTMV

Parental  SHSRPVGHCLEAATVLSKEGVECEVINLRTIRPMDIETIEASVMKTNHLVTVEGGWPQFGVG-AEICARI
          SHSRPVG.CLEAATVLS.EGVE.EV.NL.TIRPMDI..IEA.VMKT.HLVTVEGG.P.FGV...EIC.R.
Retrocopy SHSRPVGPCLEAATVLSNEGVE*EVTNLHTIRPMDIKAIEANVMKTQHLVTVEGGCPPFGVD<SEICVRN

Parental  MEGPAFNFLDAPAVRVTGADIPMPYAKILEDNSVPQVKDIIFAIKKTLN
          ...P...FLD.PAV...GAD.PMP.A.IL.DN..PQVKDIIFA.KK.LN
Retrocopy IQCPILKFLDTPAVCIAGADVPMPHAEILGDNCAPQVKDIIFAVKKILN

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	155.96 RPM
SRP012922_cerebellum	0.00 RPM	134.17 RPM
SRP012922_heart	0.00 RPM	220.66 RPM
SRP012922_kidney	0.00 RPM	159.90 RPM
SRP012922_liver	0.00 RPM	61.92 RPM
SRP012922_lung	0.00 RPM	56.66 RPM
SRP012922_quadricep_muscle	0.00 RPM	228.99 RPM
SRP012922_spleen	0.00 RPM	62.61 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_1090 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021724	1 retrocopy	retro_btau_596,
Canis familiaris	ENSCAFG00000007340	2 retrocopies	retro_cfam_1215, retro_cfam_2031,
Callithrix jacchus	ENSCJAG00000019739	1 retrocopy	retro_cjac_3875,
Dasypus novemcinctus	ENSDNOG00000006937	1 retrocopy	retro_dnov_1090 ,
Monodelphis domestica	ENSMODG00000002398	1 retrocopy	retro_mdom_614,
Mus musculus	ENSMUSG00000021748	1 retrocopy	retro_mmus_290,
Oryctolagus cuniculus	ENSOCUG00000015632	1 retrocopy	retro_ocun_342,
Procavia capensis	ENSPCAG00000016595	1 retrocopy	retro_pcap_261,
Sarcophilus harrisii	ENSSHAG00000008480	1 retrocopy	retro_shar_5,
Ictidomys tridecemlineatus	ENSSTOG00000019553	2 retrocopies	retro_itri_1349, retro_itri_249,
Tupaia belangeri	ENSTBEG00000016148	2 retrocopies	retro_tbel_1651, retro_tbel_3170,