RetrogeneDB ID: retro_dnov_2548

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_84871:2135..2477(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC17
• Ensembl ID: ENSDNOG00000000509
• Aliases: None
• Description: zinc finger, CCHC domain containing 17 [Source:HGNC Symbol;Acc:30246]

Sequence

>retro_dnov_2548
ATGAAAAATCATAGGATAAAAGTATCCCTCTCCATGAAAGTTGTAAAGCAAGGCACTGGGAAATACCTAGACACAAACTA
CATTATTACTGAGCAAGAAAAGAAGCAGAGGTGGTCCTTCCAGGATTACACGGGGCAGATCATCCTGGAGGCTGCCCAGA
ACATTACTTTCAAGAAATGTGGTTCTAAGTATACTTTGCAAAGGATTGTTTCATACAACTGGAAGTCAAGAAATACTCTG
ATACCTGATGAAGAAGAGGAGAAGAGAGACAAATCAACAGAGTTTGAGGAGACTAGTCCTATGAGAAATTCTCCTAGAAA
AGAAAGAGGAAAGAGAAAAGAA

Alignment

ORF - retro_dnov_2548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.3 %
• Parental protein coverage: 51.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKNDRIKVSLSMKVVNQGTGKDLDPNNVIIEQEERRSGPSQDYTGQKITLEAVLNTTCKKCGCK-GHFAK
          MKN.RIKVSLSMKVV.QGTGK.LD.N..I.EQE.......QDYTGQ.I.LEA..N.T.KKCG.K...FAK
Retrocopy MKNHRIKVSLSMKVVKQGTGKYLDTNYIITEQEKKQRWSFQDYTGQ-IILEAAQNITFKKCGSK<VYFAK

Parental  DCFMQPGGTKYS-LIPDEEEEKQEAKSAEFEKPDPTKNSSRKRKKEKKK
          DCF.Q....KYS.....EEE.....KS.EFE...P..NS.RK.....K.
Retrocopy DCFIQLEVKKYS>IPDEEEEKRD--KSTEFEETSPMRNSPRKERGKRKE

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	11.47 RPM
SRP012922_cerebellum	0.00 RPM	40.14 RPM
SRP012922_heart	0.00 RPM	11.83 RPM
SRP012922_kidney	0.00 RPM	14.24 RPM
SRP012922_liver	0.00 RPM	3.41 RPM
SRP012922_lung	0.00 RPM	28.25 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.92 RPM
SRP012922_spleen	0.00 RPM	22.09 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_2548 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017710	1 retrocopy	retro_amel_1501,
Bos taurus	ENSBTAG00000016818	2 retrocopies	retro_btau_168, retro_btau_273,
Canis familiaris	ENSCAFG00000011131	2 retrocopies	retro_cfam_485, retro_cfam_835,
Dasypus novemcinctus	ENSDNOG00000000509	1 retrocopy	retro_dnov_2548 ,
Dipodomys ordii	ENSDORG00000004128	1 retrocopy	retro_dord_200,
Echinops telfairi	ENSETEG00000007421	1 retrocopy	retro_etel_1280,
Loxodonta africana	ENSLAFG00000015364	1 retrocopy	retro_lafr_534,
Myotis lucifugus	ENSMLUG00000000594	1 retrocopy	retro_mluc_2176,
Monodelphis domestica	ENSMODG00000017082	1 retrocopy	retro_mdom_252,
Mustela putorius furo	ENSMPUG00000015442	1 retrocopy	retro_mputfur_680,
Mus musculus	ENSMUSG00000028772	1 retrocopy	retro_mmus_2150,
Otolemur garnettii	ENSOGAG00000013749	1 retrocopy	retro_ogar_1225,
Sorex araneus	ENSSARG00000007944	1 retrocopy	retro_sara_691,
Ictidomys tridecemlineatus	ENSSTOG00000003825	1 retrocopy	retro_itri_405,