RetrogeneDB ID: retro_dnov_2271

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_60140:6159..7108(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTMR1
• Ensembl ID: ENSDNOG00000013433
• Aliases: None
• Description: myotubularin related protein 1 [Source:HGNC Symbol;Acc:7449]

Sequence

>retro_dnov_2271
TTTTGAATACAATACAAAGAAATATTTCCTGAAAATGGGGTGGAAGCTATATGATCCTCTTTCCAAGTATAGGAGGCAGG
GAATTCCTAATGAAAGCTGCAGAATAACTAAGATAAATGAACAGTAGGGGCTGTGTGATGATTACTCCACCCTCTTGGTT
GTGCCAGCAAATATTCCTGATGAAGATTTAAAGAGAGTGGCATTCTTCAGATCAAGGGGTGGGGTGGCAATTTTATCATG
GATTCATCCTGAAAGTCAAGCCACAATTGCTCAGTGTAGTTAGCCCATGGTAGGAGTGAGTGGGAAGTGGAGCAAAGAAG
ATGAAAAATACCTTCAAGCCATCATGGGTTCCAATGCCCAGTCTTATAAAATTTTTATATTCAGTGCCTGGCCAAGTGTT
AATTCCATTGACAAGAAGGCAAAGGGTGGAAGTTATGAAAGTTAAGATGCCTGTCAAAATGCAGAGCTAGTTTTTCTCCA
TATCCACAGTAATCATGATATAAGAGAATCATTATGAAAACTTGAGATTGTGTACCCCAATACTGAGGAAACTCAGTGGT
TGTCTAACTTGGAATCTACTCATTGTCTAGAATATATTAAGATTATTCTTGCAGAGGGTCTTGGGATTGCTGACAAGGTA
GAGTAAGGGAAGATGTCTGTGGTAGTACATTGCAGTGATGGTTGGAAGTGCCCAGCTTAGCTAACTTCCCTGGCCATGCT
TATGTTGAATGGATACTATAGAACCATCTAAGAATATGAAATCCTTGTGGAGAAAGAATGGCTAAGCTTTGGATGGCGAT
TTCAACTAAGAGTTGGTCATGGAGATAAGAATTATGAAGATGCAGACAGATCACCCGTTTTCCTTCAGTTCATTGACTGT
GTCTGACAAATGACAAGACAAGACAACATTTGAATTAATTTCATATTACTATTTTGGACCACCTATATA

Alignment

ORF - retro_dnov_2271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.06 %
• Parental protein coverage: 63.02 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FAFNYKEKFPING-WKVYDPIAEYKRQGLPNESWKISKINSNYELCDTYPAIIVVPTSVKDDDLSKVAAF
          F...YKE.FP.NG.WK.YDP...Y.RQG.PNES..I.KIN....LCD.Y....VVP....D.DL..VA.F
Retrocopy F*IQYKEIFPENG>WKLYDPLSKYRRQGIPNESCRITKINEQ*GLCDDYSTLLVVPANIPDEDLKRVAFF

Parental  RAKGRVPVLSWIHPESQATITRCSQPLVGPNDKRCKEDEKYLQTIMDANAQSHKLIIFDARQNSVADTNK
          R..G.V..LSWIHPESQATI..CS.P.VG...K..KEDEKYLQ.IM..NAQS.K..IF.A.........K
Retrocopy RSRGGVAILSWIHPESQATIAQCS*PMVGVSGKWSKEDEKYLQAIMGSNAQSYKIFIFSAWPSVNSIDKK

Parental  AKSGGYESESAYPNAELVFLEIHNIHVMRESLRKLKEIVYPSIDETRWFSNVDGTHWLEYIRMLLAGAVR
          AK.G.YES..A..NAELVFL.IH..H..RESL.KL.EIVYP...ET.W.SN...TH.LEYI...LA....
Retrocopy AKGGSYES*DACQNAELVFLHIHSNHDIRESL*KL-EIVYPNTEETQWLSNLESTHCLEYIKIILAEGLG

Parental  IADKIESGKTSVVVHCSDGWDRTAQLTALAMLMLDSYYRTIKGFEALIEKEWISFGHRFALRVGHGNDNH
          IADK.E.GK.SVVVHCSDGW...A.LT.LAMLML..YYRTI...E.L.EKEW.SFG.RF.LRVGHG..N.
Retrocopy IADKVE*GKMSVVVHCSDGWKCPA*LTSLAMLMLNGYYRTI*EYEILVEKEWLSFGWRFQLRVGHGDKNY

Parental  ADADRSPIFLQFIDCVWQMTRQFPSAFEFNELFLITIL
          .DADRSP.FLQFIDCV.QMTRQ......F..LF..T..
Retrocopy EDADRSPVFLQFIDCV*QMTRQDNI*INFILLFWTTYI

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	14.97 RPM
SRP012922_cerebellum	0.00 RPM	28.59 RPM
SRP012922_heart	0.00 RPM	18.33 RPM
SRP012922_kidney	0.00 RPM	10.40 RPM
SRP012922_liver	0.00 RPM	12.69 RPM
SRP012922_lung	0.00 RPM	12.22 RPM
SRP012922_quadricep_muscle	0.00 RPM	39.81 RPM
SRP012922_spleen	0.00 RPM	15.68 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_2271 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013433	1 retrocopy	retro_dnov_2271 ,
Equus caballus	ENSECAG00000007323	1 retrocopy	retro_ecab_527,
Macropus eugenii	ENSMEUG00000012257	1 retrocopy	retro_meug_1367,