RetrogeneDB ID: retro_dnov_999

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_132473:3476..4163(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC2A1
• Ensembl ID: ENSDNOG00000015043
• Aliases: None
• Description: solute carrier family 2 (facilitated glucose transporter), member 1 [Source:HGNC Symbol;Acc:11005]

Sequence

>retro_dnov_999
CTGGTCATGGGCCACTTGGTTATTGGCCTCTTATTTGGATTCTGTACAGATTTTATGTCTATGTACATTGGAGAGATATC
GCCCTCTACCTTATGGGTTGCCACGAGCACTCTTAATGAGCCAGGTATCATCATTGGGATTCTGGTGGCCCAGATCTATG
GTCTGGAAATCATCATGTGATCTGGAGAACTGTGACCTGTGCTATTAGTCTTCATCATTATTCCAGATGTCTTGCAGAGT
GTAGCCATTCAATTTTTCCCTGAAAGTCACAGATTCTTGCTCATTAATAGAAAGGAAGAAGAGTATGCCAAGCAGGTCCT
CCAGCAATTTGGAGGCATTCAGGATGTGAGCAATGACATGCAGAAGATGAAAGGTGAGATTGATAACATTTCATAAGAAA
AGAAAGCCAATATGCTGGAGCTCTTTAAAACACCCAGCTACCAGTGGCCTATCATCATTTTCACCATGCTGCAGCTATCT
CAGCAGTTCTCTAGAATCAGTGCTGTGTTTTATTACTCTCCAGGAATCTTCAGACATGTAGATGTTGAAGAAACATTCTA
TGCCATTATTGGTGCCAGTGTGATCAATACAAGCTTCACTGTGATTTCACTGTTTCTTGTGGAAAACGCAGGAAAAAAGC
CTCTACATATGCTAAGCATTGGAGGGATGGCTCTTTGTTCCAGTCTC

Alignment

ORF - retro_dnov_999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.66 %
• Parental protein coverage: 50.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LILGRFIIGVYCGLTTGFVPMYVGEVSPTALRGALGTLHQLGIVVGILIAQIFGLDSIMGNEDLWPLLLS
          L..G...IG...G..T.F..MY.GE.SP..L..A..TL...GI..GIL.AQI.GL..IM....L.P.LL.
Retrocopy LVMGHLVIGLLFGFCTDFMSMYIGEISPSTLWVATSTLNEPGIIIGILVAQIYGLEIIM*SGEL*PVLLV

Parental  IIFIPALLQCILLPLCPESPRFLLINRNEENQAKSVLKKLRGTQDVSHDLQEMKEESRQMMREKKVTILE
          .I.IP..LQ.......PES.RFLLINR.EE..AK.VL....G.QDVS.D.Q.MK.E......EKK...LE
Retrocopy FIIIPDVLQSVAIQFFPESHRFLLINRKEEEYAKQVLQQFGGIQDVSNDMQKMKGEIDNIS*EKKANMLE

Parental  LFRSPIYRQPILIAVVLQLSQQLSGINAVFYYSTSIFEKAGVQQPVYATIGSGIVNTAFTVVSLFVVERA
          LF..P.Y..PI.I...LQLSQQ.S.I.AVFYYS..IF....V....YA.IG....NT.FTV.SLF.VE.A
Retrocopy LFKTPSYQWPIIIFTMLQLSQQFSRISAVFYYSPGIFRHVDVEETFYAIIGASVINTSFTVISLFLVENA

Parental  GRRTLHLIGLAGMAGCAVL
          G...LH.....GMA.C..L
Retrocopy GKKPLHMLSIGGMALCSSL

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	21.78 RPM
SRP012922_cerebellum	0.00 RPM	29.14 RPM
SRP012922_heart	0.00 RPM	4.87 RPM
SRP012922_kidney	0.00 RPM	3.83 RPM
SRP012922_liver	0.00 RPM	0.15 RPM
SRP012922_lung	0.00 RPM	5.96 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.21 RPM
SRP012922_spleen	0.00 RPM	1.14 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_999 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015043	1 retrocopy	retro_dnov_999 ,
Ictidomys tridecemlineatus	ENSSTOG00000021861	1 retrocopy	retro_itri_89,