RetrogeneDB ID: retro_dnov_1540

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_23145:3598..4220(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9orf78
• Ensembl ID: ENSDNOG00000019214
• Aliases: None
• Description: chromosome 9 open reading frame 78 [Source:HGNC Symbol;Acc:24932]

Sequence

>retro_dnov_1540
GCTGTGGCCCTGCTGTTGGGAGAGAAAGTACAGGAAGAGACCACTCTAGAGGATGATCCCTTTTAGATGAAGACAGATGG
TGTGGTGGACATGAGGAAACTGAAGGAGAGGGGCAAGATAAGATCAGTGAAGAGGAAGACCTCCACCTGGGGATGTCATT
TTCTGCGGAAACCAACCAAAGGGATGAAGATGCAGACTTGATGAAGTACACTGAAACAGAGCTTAAGAAGAGGAAAGGGA
CTGTGGAATATTAGGAACAGAAAGTAAAGCTGAAGAATGCAGAAGATCATCTTTATGAACTTCCAGAAAATATCTGTGTT
TCCTCAGGAAGGAAAGCCAAGGCAATGCTTTCCAACAAGATGCTGAGTGGCATCCCCAAGGTGACCTTGGCATCAACGCT
AAAATTAAAAATATCATTTCCACAGAGGATGCCAAGGCCCATCTGCTTGCAAAGCAGCAGCACAGCAAGAAAGACAGTGA
GACATCCTTTGTGCCCACTAACATGGCTGTAAATTACATACAGCACGACCAATTATATCATGAAGAGCTCAATGCCCCCA
TATGGAGAAACAAAGAACCCAAAGCCCAGCCTTTGAGAGTGGACGACATGGAGAAGCCAGAG

Alignment

ORF - retro_dnov_1540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.57 %
• Parental protein coverage: 86.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVALLVGEKVQEETTLVDDPFQMKTGGMVDMKKLKERGK-DKISEEEDLHLGTSFSAETNRRDEDADMMK
          AVALL.GEKVQEETTL.DDPF.MKT.G.VDM.KLKERGK.DKISEEEDLHLG.SFSAETN.RDEDAD.MK
Retrocopy AVALLLGEKVQEETTLEDDPF*MKTDGVVDMRKLKERGK<DKISEEEDLHLGMSFSAETNQRDEDADLMK

Parental  YIETELKKRKGIVEHEEQKVKPKNAEDCLYELPENIRVSSAKKTEEMLSNQMLSGIPEV-DLGIDAKIKN
          Y.ETELKKRKG.VE..EQKVK.KNAED.LYELPENI.VSS..K...MLSN.MLSGIP.V.DLGI.AKIKN
Retrocopy YTETELKKRKGTVEY*EQKVKLKNAEDHLYELPENICVSSGRKAKAMLSNKMLSGIPKV<DLGINAKIKN

Parental  IISTEDAKARLLAEQQNKKKDSETSFVLT-MAVNYVQHNRFYHEELNAPIRRNKEEPKARPLRVGDTEKP
          IISTEDAKA.LLA.QQ..KKDSETSFV.T.MAVNY.QH...YHEELNAPI.RNK.EPKA.PLRV.D.EKP
Retrocopy IISTEDAKAHLLAKQQHSKKDSETSFVPTNMAVNYIQHDQLYHEELNAPIWRNK-EPKAQPLRVDDMEKP

Parental  E
          E
Retrocopy E

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	41.42 RPM
SRP012922_cerebellum	0.00 RPM	31.62 RPM
SRP012922_heart	0.00 RPM	18.56 RPM
SRP012922_kidney	0.00 RPM	29.84 RPM
SRP012922_liver	0.00 RPM	21.98 RPM
SRP012922_lung	0.00 RPM	49.48 RPM
SRP012922_quadricep_muscle	0.00 RPM	17.31 RPM
SRP012922_spleen	0.11 RPM	54.83 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_1540 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 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Callithrix jacchus	ENSCJAG00000020318	3 retrocopies	retro_cjac_1757, retro_cjac_2299, retro_cjac_2778,
Dasypus novemcinctus	ENSDNOG00000019214	1 retrocopy	retro_dnov_1540 ,
Homo sapiens	ENSG00000136819	3 retrocopies	retro_hsap_2872, retro_hsap_2913, retro_hsap_320,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Macaca mulatta	ENSMMUG00000003795	2 retrocopies	retro_mmul_1460, retro_mmul_1870,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518,
Nomascus leucogenys	ENSNLEG00000017658	3 retrocopies	retro_nleu_1763, retro_nleu_614, retro_nleu_823,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Pan troglodytes	ENSPTRG00000021465	3 retrocopies	retro_ptro_1943, retro_ptro_1969, retro_ptro_258,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,