RetrogeneDB ID: retro_dnov_51

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1019:210283..210877(-)
• Located in intron of: ENSDNOG00000008173

Retrocopy information

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

Parental gene information

• Parental gene symbol: CA2
• Ensembl ID: ENSDNOG00000005408
• Aliases: None
• Description: carbonic anhydrase II [Source:HGNC Symbol;Acc:1373]

Sequence

>retro_dnov_51
CATCACTGGGGAGACAGCAAGCACAATGGACCCAAGCACTGGCCTGAGACATTCCCCATTGCCAAGTCAGAGTATCAATC
TCCTTTAGACATTAAAACCTAAGCAGCCAAGCACCACTCTGCCCTGTAGCCTCTATGCATTTGCTGTAAGGAAGTGATAT
CTTGGAAGATCCTCAACAATGGTCACACTTTCAAGCTGGAGTTTGATGACTCCCAGGACAAAGCAGTGCGGAAAGAAGGA
CCCTTCACTGACACTTAGAGAGTGACTCAGTTTCATTTTCACTGGGGATCTTCTGATAAGCAAGGTTCTTAGTGTACTGT
GGACAAAAAGAAATATGCTACAGAGCAGTAGCTGGTTCATTGGAACACCAAATATGGGGATTTTGGAAAAAGCATGCAAC
AACCTGATGGACTAGTTGTTTGTGGGTATTTTTTTGAAGGTTGGCAGTGCTAAACTAGGCTGTCAGAAAGTTACTGATGT
CCTAGATTCCATTAAAACAAAGGGTAGAGCCTTGAATTCACTAACTTTGATCCTCATGGCCTCCTTCCTGAGAGCTTAGA
CTACTGGACCTATCCAGGCTCACTAACCACCCCC

Alignment

ORF - retro_dnov_51 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.5 %
• Parental protein coverage: 76.15 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NHWGYSKHNGPEHWHKTFPLADGERQSPVDIDTAAVKHDPALQPLSIHYEEASSQKILNSGHSFSVEFDD
          .HWG.SKHNGP.HW..TFP.A..E.QSP.DI.T.A.KH..AL.PL.I...E..S.KILN.GH.F..EFDD
Retrocopy HHWGDSKHNGPKHWPETFPIAKSEYQSPLDIKT*AAKHHSAL*PLCICCKEVISWKILNNGHTFKLEFDD

Parental  SQDKAVLKGGPLTGTYRLIQFHFHWGSSDHEGSEHSVDKQKYAAELHFVHWNTKYGEFKKAVEHPDGLAV
          SQDKAV.K.GP.T.T.R..QFHFHWGSSD..GS...VDK.KYA.E...VHWNTKYG.F.K....PDGL.V
Retrocopy SQDKAVRKEGPFTDT*RVTQFHFHWGSSDKQGS*CTVDKKKYATEQ*LVHWNTKYGDFGKSMQQPDGLVV

Parental  -LGIFLKVGSARPGLQKVVDVLDSIKAKGK-SAAFTDFDPTGLLPEKLDYWTYPGSLTTP
          ..GIFLKVGSA..G.QKV.DVLDSIK.KG..S..FT.FDP.GLLPE.LDYWTYPGSLTTP
Retrocopy >VGIFLKVGSAKLGCQKVTDVLDSIKTKGR<SLEFTNFDPHGLLPESLDYWTYPGSLTTP

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	7.39 RPM
SRP012922_cerebellum	0.00 RPM	47.84 RPM
SRP012922_heart	0.46 RPM	2.32 RPM
SRP012922_kidney	0.00 RPM	264.76 RPM
SRP012922_liver	0.00 RPM	22.76 RPM
SRP012922_lung	0.00 RPM	29.93 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.46 RPM
SRP012922_spleen	0.00 RPM	343.73 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_51 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	ENSDNOG00000005408	1 retrocopy	retro_dnov_51 ,
Dasypus novemcinctus	ENSDNOG00000010755	1 retrocopy	retro_dnov_512,
Sarcophilus harrisii	ENSSHAG00000008895	1 retrocopy	retro_shar_121,