RetrogeneDB ID: retro_dnov_1477

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_21271:85755..86453(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ST6GALNAC3
• Ensembl ID: ENSDNOG00000004293
• Aliases: None
• Description: ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 [Source:HGNC Symbol;Acc:19343]

Sequence

>retro_dnov_1477
GAACCTTTGCAACTGGACTGTGACCTTTGTGCCACAGTATCAAACTCCAGTCAACTTGTTGGCCCTGAAGGTGGGGAAGG
AGAGAGATTACTCCTCCTGGATTTGGAGAATGAACAATGCCCCCACCAAGGGCTATGATGTTGGCTGAATGATGATGATT
TGGATTGTGTCCAATACCAGTGTTCCCCTTTTATTAAAAAAACATGACTATTTTTCAAAGGAAGCAAACACTACTATTTG
TGTTATATGGGGCCCTTTCCACAATATGAGGAAAGAAGGCAATGACATCATTTATAACATGTTGAAAAATACGGTTGACA
TCTATCCAAATGCCCAGATTTTTGTGACTACAGAGAAGTGCATGAGCTACTGTGATGGAACTTTGAAATAGGAGACAGGG
AAAGACAGAGTCAAGTCCAGCTTTTATCTCAGCACAGGGTGGTTTACCTTCATTCTAGCCATGGATGCCTATTACAGCAT
TCATGTCTAAGGGATGATAAATGACACCTCCTGCAAGACAGAAGGGTATAGAAAAAAACCCATACTATTTCTATGAACAA
GGCAGAAATGAGTGTGATGATTATTTTCTTCATGAACATGCCCCATATGGGGGGCATATGTTTATCACTGAAAAGAAAGT
GTTTACTAAGTGGGCCAAGAAAGACAGGATAATATTTATACACCTAAACTGGATGGTG

Alignment

ORF - retro_dnov_1477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.51 %
• Parental protein coverage: 78.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EPLQLDCDLCAIVSNSGQMVGQ-KVGKEIDRSSCIWRMNNAPTKGYEEDVGHMTMIRVVSHTSVPLLLKN
          EPLQLDCDLCA.VSNS.Q.VG..KVGKE.D.SS.IWRMNNAPTKGY..DVG.M.MI..VS.TSVPLLLK.
Retrocopy EPLQLDCDLCATVSNSSQLVGP>KVGKERDYSSWIWRMNNAPTKGY--DVG*MMMIWIVSNTSVPLLLKK

Parental  PDYFFKEANTTIYVIWGPFRNMRKDGNGIVYNMLKKTVDIYPNAQIYVTTEKRMSYCDGVFKQETGKDRV
          .DYF.KEANTTI.VIWGPF.NMRK.GN.I.YNMLK.TVDIYPNAQI.VTTEK.MSYCDG..K.ETGKDRV
Retrocopy HDYFSKEANTTICVIWGPFHNMRKEGNDIIYNMLKNTVDIYPNAQIFVTTEKCMSYCDGTLK*ETGKDRV

Parental  QSGSYLSTGWFTFILAMDACYSIHVYGMINDTYCKTEGYRKV-PYHYYEQGRDECDEYFLHEHAPYGGHR
          .S..YLSTGWFTFILAMDA.YSIHV.GMINDT.CKTEGYRK..PY..YEQGR.ECD.YFLHEHAPYGGH.
Retrocopy KSSFYLSTGWFTFILAMDAYYSIHV*GMINDTSCKTEGYRKK>PYYFYEQGRNECDDYFLHEHAPYGGHM

Parental  FITEKKVFTKWAKKHRIIFTHPNWTV
          FITEKKVFTKWAKK.RIIF.H.NW.V
Retrocopy FITEKKVFTKWAKKDRIIFIHLNWMV

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	0.19 RPM
SRP012922_cerebellum	0.00 RPM	2.06 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	7.67 RPM
SRP012922_liver	0.00 RPM	0.15 RPM
SRP012922_lung	0.00 RPM	11.00 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.17 RPM
SRP012922_spleen	0.00 RPM	1.37 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_1477 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004293	1 retrocopy	retro_dnov_1477 ,