RetrogeneDB ID: retro_dnov_2621

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_91419:4275..4824(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUGT1
• Ensembl ID: ENSDNOG00000002991
• Aliases: None
• Description: SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae) [Source:HGNC Symbol;Acc:16987]

Sequence

>retro_dnov_2621
ACAGAACCTCAGGCGATCCTGACGCTTAGCTCGAGGATGTGCCGAAGAGCAAAGCACATGTGGAGTGTTCAGAAAAAAGA
TTTTCCTCTTTGGTGAAACCTCTTTCTAGAGAGGATTACAGTTTGAGACTGAGACTTCTGCACCCTATGATACCAGAACA
GAACACATTTAAAGTACTTTCAAGAAAGATTGAAATTAAAATGGAAAAGCAGAGGCTGTGACATGGGAAAAGCTAGAGGG
AGGAGACATACCTAAGCCAAAACAGTTCATTGCGATGTAAAGAACCTATATCCATTATCACCTCATTACACAAAAAAATG
GGATAAATTGGTTAGCAAGATCAAAGAAAAGAATGAGAAGCTGGAGGGAGATGCAGAATTAAACAGATTGTTTCAGCAAA
TCTATTCAGATGTTTCTGACGAAGTGAAACGTGTCCTGAACAAATCATTTATGGAGTCTAGTGGCACGGTTTTGAGTACC
AACTGGTCTGATGTAGGTAAAAGGAATGTTGAAGTCAATCCTCCTGATGATATGGAATGGAAAAAGTAC

Alignment

ORF - retro_dnov_2621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.74 %
• Parental protein coverage: 51.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TESQVIITLM-IKNVQKNDVNVEFSEKEFSALVKLPSGEDYNLKLRLLHPIIPEQSTFKVLSTKIEIKMK
          TE.Q.I.TL.....V.K....VE.SEK.FS.LVK..S.EDY.L.LRLLHP.IPEQ.TFKVLS.KIEIKM.
Retrocopy TEPQAILTLS<LEDVPKSKAHVECSEKRFSSLVKPLSREDYSLRLRLLHPMIPEQNTFKVLSRKIEIKME

Parental  KP-EAVRWEKLEGEGDTSKPKQFIA-DVKNLYPSSSHYTRNWDKLVCEIKEEEKNEKLEGDAALNKLFQQ
          K..EAV.WEKLEG.GD..KPKQFIA.DVKNLYP.S.HYT..WDKLV..IKE..KNEKLEGDA.LN.LFQQ
Retrocopy KQ<EAVTWEKLEG-GDIPKPKQFIA<DVKNLYPLSPHYTKKWDKLVSKIKE--KNEKLEGDAELNRLFQQ

Parental  IYSDGSDEVKRAMNKSFMESGGTVLSTNWSDVGKRKVEINPPDDMEWKKY
          IYSD.SDEVKR..NKSFMES.GTVLSTNWSDVGKR.VE.NPPDDMEWKKY
Retrocopy IYSDVSDEVKRVLNKSFMESSGTVLSTNWSDVGKRNVEVNPPDDMEWKKY

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	0.78 RPM	20.61 RPM
SRP012922_cerebellum	0.14 RPM	19.11 RPM
SRP012922_heart	0.00 RPM	20.19 RPM
SRP012922_kidney	0.00 RPM	23.82 RPM
SRP012922_liver	0.00 RPM	12.23 RPM
SRP012922_lung	0.00 RPM	25.20 RPM
SRP012922_quadricep_muscle	0.00 RPM	17.14 RPM
SRP012922_spleen	0.00 RPM	22.43 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_2621 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008606	2 retrocopies	retro_amel_353, retro_amel_896,
Canis familiaris	ENSCAFG00000004823	1 retrocopy	retro_cfam_136,
Callithrix jacchus	ENSCJAG00000003604	1 retrocopy	retro_cjac_310,
Cavia porcellus	ENSCPOG00000003374	1 retrocopy	retro_cpor_110,
Dasypus novemcinctus	ENSDNOG00000002991	1 retrocopy	retro_dnov_2621 ,
Homo sapiens	ENSG00000165416	1 retrocopy	retro_hsap_2628,
Gorilla gorilla	ENSGGOG00000006797	1 retrocopy	retro_ggor_1840,
Nomascus leucogenys	ENSNLEG00000015700	1 retrocopy	retro_nleu_640,
Otolemur garnettii	ENSOGAG00000008220	1 retrocopy	retro_ogar_41,
Pan troglodytes	ENSPTRG00000005906	1 retrocopy	retro_ptro_1773,