RetrogeneDB ID: retro_dnov_1975

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_39912:178..825(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZC3H8
• Ensembl ID: ENSDNOG00000018056
• Aliases: None
• Description: zinc finger CCCH-type containing 8 [Source:HGNC Symbol;Acc:30941]

Sequence

>retro_dnov_1975
AATGATGATAATCTTCAGGAAGCAGATGATAATTTGTCAAAGAGCTTAGGCAGTATAGACAAGCTAAGGAAATGGCAGAT
ATACCTGGTTCTTATCATTTCCTGAAGTGTCTATGAAGAAAGAGGGGGTGAATGACACCCAGCAAACCGTTAAACAAACA
AACAAAAATCATACAGTTGGCTATAAGCATGGGAAACAGAAGGAAACAAAGGGAGAATGGGCTGGCCCTGGAAACAAGGA
TCAAATGCTTTCCCGAGGAAAATTGCTAATGGAGGAGGAGGACAAACCCGAAGAGAAGTGGCAGCCTTTGATGATGAGCC
ACCATCCACCAACGTACAGCAGAACGCAAAGGAAAACACATTTGAAATGTTTTCTGGAAAGGAAAGGTATCAAGGATGAC
CCGTGTAAATCTGTTCATGGTGCAGAGTTGAGTAGAAATAAGATCCGGGTAAGTTTTATGTTCAGGGATTTTGTACCCGC
GGTGAAAACTGCCTGTAGTTGCGAAGTGAATTTCCATGCACGTTTTACTATAAAGGATGGAGGGTTATCAGGGAGAATAT
AGCAAGTTTTCTCATCCTCCGCTGACTGCTGAGACACAAAAACTGCTGGCTAGAGTTCTGGATGCTGAAAACAAGTCCTC
GTGTAAA

Alignment

ORF - retro_dnov_1975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.95 %
• Parental protein coverage: 89.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SDDNLCSQESEDT-FAEELQQYIQAKEMANT-TQTLPFPEGPVKKEGVNSTLQAVKQKNKNLKAGRKKGK
          .DDNL..QE..D..F..EL.QY.QAKEMA...T..L.FPE...KKEGVN.T.Q.VKQ.NKN...G.K.GK
Retrocopy NDDNL--QEADDN<FVKELRQYRQAKEMADI<TWFLSFPEVSMKKEGVNDTQQTVKQTNKNHTVGYKHGK

Parental  QKKMKRKQAGTGNK-GSNAFLRKNG-LQDEGDKE-KQQRVKMSQGFINQHTVERKGKQICKYFLERKCIK
          QK..K...AG.GNK.GSNAF.RK......E...E.K.Q...MS..........RK....C..FLERK.IK
Retrocopy QKETKGEWAGPGNK<GSNAFPRKIA>MEEEDKPEEKWQPLMMSHHPPTYSRTQRKTHLKC--FLERKGIK

Parental  GDQCKFDHDAEIEKKK-EMCKFYVQGYCTRGENCLYLHNEYPCKFYHTGTKC-YQGEYCKFSHAPLTAET
          .D.CK..H.AE....K....KFYVQG.CTRGENCL.L..E.PC.FY..G....YQGEY.KFSH.PLTAET
Retrocopy DDPCKSVHGAELSRNK<DPGKFYVQGFCTRGENCL*LRSEFPCTFYYKGWRV<YQGEYSKFSHPPLTAET

Parental  QELLARVLDTEKKSTCQ
          Q.LLARVLD.E.KS.C.
Retrocopy QKLLARVLDAENKSSCK

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	27.08 RPM
SRP012922_heart	0.00 RPM	3.94 RPM
SRP012922_kidney	0.00 RPM	10.68 RPM
SRP012922_liver	0.00 RPM	4.80 RPM
SRP012922_lung	0.00 RPM	15.58 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.92 RPM
SRP012922_spleen	0.00 RPM	12.93 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_1975 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008258	1 retrocopy	retro_cpor_28,
Dasypus novemcinctus	ENSDNOG00000018056	1 retrocopy	retro_dnov_1975 ,
Oryctolagus cuniculus	ENSOCUG00000011253	1 retrocopy	retro_ocun_1773,
Otolemur garnettii	ENSOGAG00000002554	2 retrocopies	retro_ogar_1723, retro_ogar_2745,