RetrogeneDB ID: retro_dnov_1902

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_36096:4926..5438(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATXN7L3
• Ensembl ID: ENSDNOG00000003379
• Aliases: None
• Description: ataxin 7-like 3 [Source:HGNC Symbol;Acc:25416]

Sequence

>retro_dnov_1902
GGGTTCTGTCTTGAGGTCCACCGAGCTGTAAAGTGTGGATAATTCTTCCTGGACCCCACAGGCCCTGATGCATGAAGGAT
TTTGAGATCGTGGACCAAATGGAGTTTGGACATCTTTGAACATGTTTTCAACCAATGGACTAGCAAGGAGTGTATTTGCC
CAATTGCAGTCCCAGCATCATTGCCTCCAGCTTTGCTCTCCATCTGGAGAAGTGCTGGGAATGGGTGGAACAGCATCCAC
ACATTGCAGGCTCCAGGTTGCCAATAGCAACAGTATGAGCAAGTCTGAAAGTGACCAAGAGGAAGATGATGGCATCAATG
GCAACGACTGGTCCTATGGCTTGAGAAGAAAGCCAAGAAGAGAGCGTTAGTAAGAACCCCAATTCCCCTTGAACTAAGTA
ATCAAAACACAAAAACACTGGGTTTAACATTTCAGATTCTTGTAAGCATAACAACTCCACTGGGAAGAGCTATGACACCC
TGGGGTCAGAGGAGCTGTGTGGCCTGCTCAGC

Alignment

ORF - retro_dnov_1902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.92 %
• Parental protein coverage: 93.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GIC-EVHRAVKCGYFFLDDTDPDS-MKDFEIVDQP-GLDIFGQVFNQWKSKECVC-PNCSRSIAASRFAP
          G.C.EVHRAVKCG.FFLD.T.PD..MKDFEIVDQ...LDIF..VFNQW.SKEC.C.PNCS.SI.AS.FA.
Retrocopy GFCLEVHRAVKCG*FFLDPTGPDA<MKDFEIVDQM>SLDIFEHVFNQWTSKECIC<PNCSPSIIASSFAL

Parental  HLEKC-LGMGRNSSRIANRRIANSNNMNKSESDQEDNDDINDNDWSYG-SEKKAKKR-KSDKNPNSPRRS
          HLEKC.LGMG...S.......ANSN.M.KSESDQE..D.IN.NDWSYG..EKKAKKR....KNPNSP...
Retrocopy HLEKC<LGMGGTASTHCRLQVANSNSMSKSESDQEEDDGINGNDWSYG<LEKKAKKR<SVSKNPNSP-*T

Parental  KSLKHKNGELSNSDPFKYNNSTGISYETLGPEELRSLLT
          K..KHKN.....SD..K.NNSTG.SY.TLG.EEL..LL.
Retrocopy K*SKHKNTGFNISDSCKHNNSTGKSYDTLGSEELCGLLS

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	6.22 RPM
SRP012922_cerebellum	0.00 RPM	10.59 RPM
SRP012922_heart	0.00 RPM	2.32 RPM
SRP012922_kidney	0.00 RPM	2.46 RPM
SRP012922_liver	0.00 RPM	3.41 RPM
SRP012922_lung	0.00 RPM	5.65 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.21 RPM
SRP012922_spleen	0.11 RPM	4.92 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_1902 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 5 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003379	13 retrocopies	retro_dnov_1026, retro_dnov_1144, retro_dnov_1211, retro_dnov_1590, retro_dnov_1902 , retro_dnov_2325, retro_dnov_2448, retro_dnov_2497, retro_dnov_2600, retro_dnov_516, retro_dnov_86, retro_dnov_867, retro_dnov_961,
Homo sapiens	ENSG00000087152	1 retrocopy	retro_hsap_4847,
Gorilla gorilla	ENSGGOG00000010959	1 retrocopy	retro_ggor_3023,
Myotis lucifugus	ENSMLUG00000006416	1 retrocopy	retro_mluc_41,
Macaca mulatta	ENSMMUG00000029935	1 retrocopy	retro_mmul_820,