RetrogeneDB ID: retro_dnov_2215

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_55911:3456..4250(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000005268
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TCF19
• Ensembl ID: ENSDNOG00000003961
• Aliases: None
• Description: transcription factor 19 [Source:HGNC Symbol;Acc:11629]

Sequence

>retro_dnov_2215
CACGCGAAGCTGCATGCAGAGCGCCGGGGCGATGGCTGGAGGGTCAGCCTGGAGGACCCGAGCAACCAAGGGACCTTGGT
CAACAATGTCCAACTCCCAAGAGGTCACAGGCTGGAGTTGAGCGATGGTGACCTCCTGATCTTTGGCCCCGAGGGGTTGC
CAGGAACCAGCCCCTCAAAGTTCTACTTCATGTTCCAGCAAGTCCGAGTCAAACCTCAAGACTTTGCTGCCATCACCACC
CCCCGGGTCGACGGGAGAAGAGGGGGCCAGGGGTGGCTTCCAGCCCATGCTGCCCTCCCGGGGGACCCCACAGAGGCCCC
TCAGCACCCCAAAGTCCACACTGATTCTCAACTCCATCGGCAGCTTCAGCAAGCTCCGGCCCCAGCCCCTCACCTTCTCC
AGGAGCGGGGCTGGGGCGGGGCTTGTCCCTGCCCACCCCCCATGGGGAAGAGGGGAGCCCGCCTTCCGCCCCGGCCCTGG
TTCCCAGAAGCCGGAAGAAATCGGCCCACCGAGTGCTGGCGGAGCTGGAAGACGAAAGGGGGTCCCCCGAAAGCCCCCCA
CCCGAGCACACAGAGCCTAGGAAGAAACTGCGCGGAGAGAAGTCACCGCTGACGCCCAGCGGAAATCGTCGTGGCTGTCC
TCGGAAGCACCCAGTGAGCACCCCTGCGTTTGGGGACGGGGATCCCTGTGCAGCCCCTCGCTGCCGCCTGCCCCGGGAGG
AGCCGGTGGCCTGGCTTCAGTGTGATGGCTGTGACATTTGGTTCCACGTGGCCTGTGTTGGCTGCAGCTTCCAG

Alignment

ORF - retro_dnov_2215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.48 %
• Parental protein coverage: 82.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HAELHAERRGDGWRVSLEDLSSQGTLVNNVRIPRGHRLELSDGDLLTFGPEGLPGTSPSEFYFMFQQVRV
          HA.LHAERRGDGWRVSLED.S.QGTLVNNV..PRGHRLELSDGDLL.FGPEGLPGTSPS.FYFMFQQVRV
Retrocopy HAKLHAERRGDGWRVSLEDPSNQGTLVNNVQLPRGHRLELSDGDLLIFGPEGLPGTSPSKFYFMFQQVRV

Parental  KPQDFAAITTPR-SRGEEGAGGGFRPMLPSRGTPQRPLSTPKSTLILNSIGSLSKLRPQPLTFSRS-GAG
          KPQDFAAITTPR.S.GEEGA.GGF.PMLPSRGTPQRPLSTPKSTLILNSIGS.SKLRPQPLTFSRS.G.G
Retrocopy KPQDFAAITTPR>STGEEGARGGFQPMLPSRGTPQRPLSTPKSTLILNSIGSFSKLRPQPLTFSRS>GLG

Parental  REPQGLSLPTPHGEAGSPPSAPPPAPRNRRKSAHRVLAELEDERGSPESPPPEHTEPRKKLRGEKSPLTP
          R...GLSLPTPHGE.GSPPSAP...PR.R.KSAHRVLAELEDERGSPESPPPEHTEPRKKLRGEKSPLTP
Retrocopy R---GLSLPTPHGEEGSPPSAPALVPRSRKKSAHRVLAELEDERGSPESPPPEHTEPRKKLRGEKSPLTP

Parental  SGNRRGRPRKHPASTPAFGGGEPCAAPRCRLPQEEPVAWVQCDGCEVWFHVACVGCSFQ
          SGNRRG.PRKHP.STPAFG.G.PCAAPRCRLP.EEPVAW.QCDGC..WFHVACVGCSFQ
Retrocopy SGNRRGCPRKHPVSTPAFGDGDPCAAPRCRLPREEPVAWLQCDGCDIWFHVACVGCSFQ

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	8.17 RPM
SRP012922_cerebellum	0.14 RPM	5.09 RPM
SRP012922_heart	0.23 RPM	1.16 RPM
SRP012922_kidney	0.27 RPM	1.64 RPM
SRP012922_liver	0.00 RPM	0.93 RPM
SRP012922_lung	0.00 RPM	1.83 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.90 RPM
SRP012922_spleen	0.46 RPM	18.66 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_2215 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003961	1 retrocopy	retro_dnov_2215 ,