RetrogeneDB ID: retro_dnov_1829

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_32297:43516..44195(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000006963
• Aliases: None
• Description: None

Sequence

>retro_dnov_1829
GTTGAAAGTAAAAGGACAATTTACCTCCTTCATAGGATTACAAGTGCTCCTGATATGGAAGAAACACTGAATGAATCAGA
AATTAAGGTGGATGGTGTCAGACAAAAGATACTGCAGGTAGCCCAAGGCTATCAGGAGAAGACATGCGTCAGTTTCATTG
AACCATTACTACAGGACTGCTGGATTATGTGCAGGCTGTCTCTTTCCGGCACTTTATCAAAATACAATCATTAATTAGTA
TGGATGAAATTAATAAACAATTGATATTTACGAAAGAAGACAAAAGAAAGAAAATGAGACCCTCTCTTCTGATGCACAGG
ATGAGCGATCTGAAACGTGGTGCCTGAGAGTCGCACCCATTGATTATCTTCTCGGAGTGGCTGATTTAACCGGAGAATTG
ATGCAGATGTGTATTAACAGGGTGGGGAATGGGAACATTGACACCCCCTTTTAAGTGAGCCACATTTTACATCAGGTTTA
TAATGGGATTTCACTCATTGGCCACACTGGACCTTATGAGGTTTCTAAGAAGCTATATACCTTGAAGCAAAGTCTGACCA
AAATAGAGAATGCTTGTTATGACTTGAAAGTCAGAGGTTCAGAAATCCTAAACCATATGTTGACAGATGTGCTGTTTTCA
GTTAAAACAGAAATAATTGTTCAAGAGGAGAGCATTTCT

Alignment

ORF - retro_dnov_1829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.6 %
• Parental protein coverage: 77.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VESKRTIFLLHRITSAPDMEEILTESEIKLDGVRQKILQVAQ-ELSGEDMHQFHRAITTGLQEYVEAVSF
          VESKRTI.LLHRITSAPDMEE.L.ESEIK.DGVRQKILQVAQ..LSGEDM.QFH..ITTGL..YV.AVSF
Retrocopy VESKRTIYLLHRITSAPDMEETLNESEIKVDGVRQKILQVAQ<RLSGEDMRQFH*TITTGLLDYVQAVSF

Parental  QHFIKTRSLISMDEINKQLIFTTED-DGKENKTLSSDAQDKQSETWSLKVTPVDYLLGVADLTGELMRMC
          .HFIK..SLISMDEINKQLIFT.ED...KEN.TLSSDAQD..SETW.L.V.P.DYLLGVADLTGELM.MC
Retrocopy RHFIKIQSLISMDEINKQLIFTKED<QKKENETLSSDAQDERSETWCLRVAPIDYLLGVADLTGELMQMC

Parental  INSVENGDIDTPFEVSQFLRQIYDGFSFISNTGPYEVSKKLYTLKQSLAKVENACYALKVRGSEIPKHML
          IN.V.NG.IDTPF.VS..L.Q.Y.G.S.I..TGPYEVSKKLYTLKQSL.K.ENACY.LKVRGSEI..HML
Retrocopy INRVGNGNIDTPF*VSHILHQVYNGISLIGHTGPYEVSKKLYTLKQSLTKIENACYDLKVRGSEILNHML

Parental  ADV-FSVKTEIIDQEEGIS
          .DV.FSVKTEII.QEE.IS
Retrocopy TDVLFSVKTEIIVQEESIS

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	25.28 RPM
SRP012922_cerebellum	0.00 RPM	24.88 RPM
SRP012922_heart	0.00 RPM	16.24 RPM
SRP012922_kidney	0.00 RPM	12.05 RPM
SRP012922_liver	0.00 RPM	10.06 RPM
SRP012922_lung	0.00 RPM	13.75 RPM
SRP012922_quadricep_muscle	0.00 RPM	22.85 RPM
SRP012922_spleen	0.00 RPM	25.75 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_1829 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002637	1 retrocopy	retro_amel_1655,
Dasypus novemcinctus	ENSDNOG00000006963	1 retrocopy	retro_dnov_1829 ,
Felis catus	ENSFCAG00000028088	1 retrocopy	retro_fcat_1789,
Myotis lucifugus	ENSMLUG00000015591	1 retrocopy	retro_mluc_1131,
Mus musculus	ENSMUSG00000056820	1 retrocopy	retro_mmus_393,
Otolemur garnettii	ENSOGAG00000005575	1 retrocopy	retro_ogar_91,
Ictidomys tridecemlineatus	ENSSTOG00000024989	1 retrocopy	retro_itri_259,