RetrogeneDB ID: retro_dnov_2063

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_45256:3422..4028(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000002443
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2063
ACTCTACAGAGACATCTCTTTAAGAACTCTGAAAACACAGAAACATCAACAGAAGTGATTTGTCCAATCTGTACAGCATT
ATCTGCAGGCGATCCTAATCATGTCACGGATGACCTTGCAGGTCATCCTACATTTGAACACAGAGTCTCTAGGGATTTAG
ATGAATCAAGTGGTGTTCAACATGTATATAGAATGTTTCACCCTGGCCAAGGATTAGGAGGTCCTCATGCTTGTAGATCA
AATACAAACTTTACTAGCAGTTCTACTGCTAGACTTTCTTTTCCTCCGAGTTCATATTCTCCAAGCAATAGAGAAGCCAT
GGATCCTACAGCTGAGTTTTTATTTCATTTATCAGGAGTGAGACATTCTGCAGGAGGGGACAGCTTAATTCTTCTGACTC
TTCTGCTTCTCAGTTACAGCAATTGCAGATTCAGCTAGAATGCAGCAAGCCCAAGTAGCACAGCAACAACTGGAGACTGC
ACACAACACAATTCAGAGTATTAATACAGCGGTGTCACCACTACAATCACACAATCCACAGAAATGAACAACACAGCTAA
CACAGAAAGCAGTCAACAAACTCTCCATAATTCAGTTTATCTTGTC

Alignment

ORF - retro_dnov_2063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.35 %
• Parental protein coverage: 53.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLQEHV--TSEHAETSTEVICPICAALPGGDPNHVTDDFAAHLTLEHRAPRDLDESSGVRHVRRMFHPDR
          .LQ.H....SE..ETSTEVICPIC.AL..GDPNHVTDD.A.H.T.EHR..RDLDESSGV.HV.RMFHP..
Retrocopy TLQRHLFKNSENTETSTEVICPICTALSAGDPNHVTDDLAGHPTFEHRVSRDLDESSGVQHVYRMFHPGQ

Parental  RLGGPRARRSNMHFTSSSTGRLSSSQSSYSPSNREAMDPIAAELLSQLSGVRRSAG-GQLNSSGPSASQL
          .LGGP.A.RSN..FTSSST.RLS...SSYSPSNREAMDP.A..L...........G.GQLNSS..SASQL
Retrocopy GLGGPHACRSNTNFTSSSTARLSFPPSSYSPSNREAMDPTAEFLFHLSGVRHSAGG<GQLNSSDSSASQL

Parental  QQLQMQLQLE-RQHAQAARQQLETARNATRRTNT-SSVTTTITQSTATTNTANTESSQQTLQNSQFLL
          QQLQ...QLE..Q.AQ.A.QQLETA.N.....NT.S.VTTTITQST...NTANTESSQQTL.NS..L.
Retrocopy QQLQ--IQLE<MQQAQVAQQQLETAHNTIQSINT<SGVTTTITQSTEMNNTANTESSQQTLHNSVYLV

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	0.00 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	0.00 RPM	45.21 RPM
SRP012922_quadricep_muscle	0.00 RPM	112.68 RPM
SRP012922_spleen	0.00 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_2063 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,