RetrogeneDB ID: retro_dnov_840

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_113232:2..680(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCUN1D1
• Ensembl ID: ENSDNOG00000019073
• Aliases: None
• Description: DCN1, defective in cullin neddylation 1, domain containing 1 [Source:HGNC Symbol;Acc:18184]

Sequence

>retro_dnov_840
AACTGGAAGTTAATAGTAGTTGTTGCAACAATTTTTTCCAAAATCCTGAACTTTATATACTAGAGTATAAAAGGATCATT
GGACAGAAAGAAGTTGGAACTACTATACAATAGATACAAAGATCCTCAAGATGAAAATAAAATTGGAATACATGACATAG
AGCAGTTCTGTGATAACCTGGCACTAGATCCAGCCAGCATTATTGTGTTGATCATTGTGTGGCAGTTCAGAGTAGCAACA
CAATGTGAATTCTCCAAATAGGAGTTCATAGATAGCATGACAGAATTAGGATGTGACAGCATAGAAAAACTAAAGGCCCG
GATAACCAAGATGAAACAAGAATTGAAAGAACCAGGATGATTTAAGGATTTTTACCAGTTTGTTTTTAATTTTTTAAAGA
ATCCAGAACAAAATGAATTAGATCTCGAAATGGCCATTGCCTACTAGAATTTAGTGCTTAATGGAAGATTTAAATTCTTA
GACTTACAGAATAAATTTATTTTGGAACATTATAAATGATCAATACTGAAAGATACTTAGAATCTTCTTTTAGACTTCAG
TGCAGTGATTACAGATGACATATCTAATTATGATGAAGAAGGAGCATGGCCTGTTCTTATTGATGACTTTGTGAAATTTG
CATGCCCACGAATTGCTGGGACAAAAAGTACAACAGTG

Alignment

ORF - retro_dnov_840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.91 %
• Parental protein coverage: 87.6 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVL
          .WKL.V.....F......I..S.KGSLDRKKLE.LYNRYKDPQDENKIGI..I.QFCD.LALDPASI.VL
Retrocopy NWKLIVVVATIFSKILNFIY*SIKGSLDRKKLELLYNRYKDPQDENKIGIHDIEQFCDNLALDPASIIVL

Parental  IIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGL
          II.W.FR.ATQCEFSK.EF.D.MTELGCDSIEKLKA.I.KM.QELKEPG.............KNP.Q..L
Retrocopy IIVWQFRVATQCEFSK*EFIDSMTELGCDSIEKLKARITKMKQELKEPGXXXXXXXXXXXXXKNPEQNEL

Parental  DLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEXXXXXXXDDF
          DLEMAIAY.NLVLNGRFKFLDL.NKF.LEH.K.SI.KDT.NLLLDFS..I.DD.SNYDEE.......DDF
Retrocopy DLEMAIAY*NLVLNGRFKFLDLQNKFILEHYK*SILKDT*NLLLDFSAVITDDISNYDEEGAWPVLIDDF

Parental  VEFARPQIAGTKSTTV
          V.FA.P.IAGTKSTTV
Retrocopy VKFACPRIAGTKSTTV

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	22.56 RPM
SRP012922_cerebellum	0.00 RPM	13.33 RPM
SRP012922_heart	0.23 RPM	9.51 RPM
SRP012922_kidney	0.00 RPM	8.49 RPM
SRP012922_liver	0.00 RPM	8.67 RPM
SRP012922_lung	0.15 RPM	12.22 RPM
SRP012922_quadricep_muscle	0.35 RPM	19.21 RPM
SRP012922_spleen	0.23 RPM	28.96 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_840 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 14 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013358	14 retrocopies	retro_chof_1054, retro_chof_1129, retro_chof_1198, retro_chof_1373, retro_chof_1546, retro_chof_1728, retro_chof_2049, retro_chof_232, retro_chof_2329, retro_chof_2369, retro_chof_2373, retro_chof_479, retro_chof_767, retro_chof_812,
Callithrix jacchus	ENSCJAG00000005148	2 retrocopies	retro_cjac_1423, retro_cjac_2358,
Cavia porcellus	ENSCPOG00000022086	4 retrocopies	retro_cpor_1289, retro_cpor_756, retro_cpor_758, retro_cpor_870,
Dasypus novemcinctus	ENSDNOG00000019073	2 retrocopies	retro_dnov_1494, retro_dnov_840 ,
Echinops telfairi	ENSETEG00000000166	1 retrocopy	retro_etel_1460,
Homo sapiens	ENSG00000043093	1 retrocopy	retro_hsap_3502,
Gorilla gorilla	ENSGGOG00000010767	1 retrocopy	retro_ggor_2368,
Macaca mulatta	ENSMMUG00000010552	1 retrocopy	retro_mmul_1782,
Mustela putorius furo	ENSMPUG00000002369	1 retrocopy	retro_mputfur_919,
Mus musculus	ENSMUSG00000027708	1 retrocopy	retro_mmus_1009,
Nomascus leucogenys	ENSNLEG00000005983	1 retrocopy	retro_nleu_793,
Otolemur garnettii	ENSOGAG00000000658	1 retrocopy	retro_ogar_3499,
Pan troglodytes	ENSPTRG00000015661	1 retrocopy	retro_ptro_2374,
Tarsius syrichta	ENSTSYG00000012276	1 retrocopy	retro_tsyr_669,