RetrogeneDB ID: retro_dnov_1000

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_132631:854..1457(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCMF1
• Ensembl ID: ENSDNOG00000006752
• Aliases: None
• Description: potassium channel modulatory factor 1 [Source:HGNC Symbol;Acc:20589]

Sequence

>retro_dnov_1000
CGGGCTTGCTTCTCCTAGAGTTCATGTCCTCCCAGCAGCGGGGAAGCCGCGGGTCCTGCAGCTGCGCTTTGTCTCGGTTC
TCAGGAGGGAGATGGTCCGCAGGGAGTCAGCTTCCCTCTTCCAGCCCTGCCGCTTCGCGGTCACAGCAACCGCAGGTGCA
GCTGCAGCTGGAGCGGCAGCGGGCCCGGGCACTCGGCGGCCGCTGGGGACCGCACTCCACGGGAGCCGGCGTGCCAACAC
CAGGAGTGTCACCACGACCGTCGCCGTCCACAGCGACAACCCAACCCAGCAACACAGAGAGCAGGCAGCAAACTCTCCAG
GAGCCACGGTTTCCTTTAACGAGGCTGCAGGAGCATAAAATGTCGGAACCAGGGCGCCAGTCCAAGGAAAGCGAGCGCGC
AGAGGGCAGCCTGTGTGTCCCAGAGCTCCCTCTGTCCACTTTAGTGCCGAGGCAAGCTCGTCATGAGACCAGGGTGAGCC
CGGAGGGGGGTGGGAGGTGGGAGGTTTTGGTGCTAAGGGCTGAGTAGATATTACGCCTTTAGATGTTGTTTCAGGAAACT
AAATTTAAAAGAGAGAAATAAAGGAGATGAGCCTCCACCTCCT

Alignment

ORF - retro_dnov_1000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.33 %
• Parental protein coverage: 52.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RLSSSQSSYSPSNREAMDPIAAEL-LSQLSGVRRSAGGQLNSSGPSASQLQQLQMQLQLERQHAQA-ARQ
          R...S.SS..PS..EA..P.AA.L.LS..SG.R.SAG.QL.SS.P.AS..QQ.Q.QLQLERQ.A.A..R.
Retrocopy RACFS*SSCPPSSGEAAGP-AAAL<LSRFSGGRWSAGSQLPSSSPAASRSQQPQVQLQLERQRARA<TRR

Parental  QLETARNATRRTNTSSVTTTI-TQSTATTNTANTESSQQTLQNSQFLLTRLNDPKMSETERQSMESERAD
          .L.TA....RR.NT.SV.TT....STATT...NTES.QQTLQ...F.LTRL...KMSE..RQS.ESERA.
Retrocopy PLGTALHGSRRANTRSV-TTT>SPSTATTQPSNTESRQQTLQEPRFPLTRLQEHKMSEPGRQSKESERAE

Parental  RSLFVQELLLSTLV-REESSSSDEDDRG---EMADFGAMGCVDIMPLDVALEN-LNLKESNKGNEPPPP
          .SL.V.EL.LSTLV..E.SSS.D....G...E...FGA.G.VDI.PLDV...N.LNLKE.NKG.EPPPP
Retrocopy GSLCVPELPLSTLV<AEASSS*DQGEPGGGWEVGGFGAKG*VDITPLDVVSGN<LNLKERNKGDEPPPP

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	36.95 RPM
SRP012922_cerebellum	0.27 RPM	31.34 RPM
SRP012922_heart	0.00 RPM	40.14 RPM
SRP012922_kidney	0.00 RPM	28.47 RPM
SRP012922_liver	0.00 RPM	19.04 RPM
SRP012922_lung	0.92 RPM	45.21 RPM
SRP012922_quadricep_muscle	0.00 RPM	112.68 RPM
SRP012922_spleen	1.49 RPM	49.33 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_1000 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005786	1 retrocopy	retro_chof_1282,
Dasypus novemcinctus	ENSDNOG00000006752	2 retrocopies	retro_dnov_1000 , retro_dnov_2063,
Echinops telfairi	ENSETEG00000001809	1 retrocopy	retro_etel_1685,
Myotis lucifugus	ENSMLUG00000000979	1 retrocopy	retro_mluc_1781,
Monodelphis domestica	ENSMODG00000015567	1 retrocopy	retro_mdom_1682,
Otolemur garnettii	ENSOGAG00000034863	2 retrocopies	retro_ogar_3140, retro_ogar_397,
Vicugna pacos	ENSVPAG00000010386	1 retrocopy	retro_vpac_650,