RetrogeneDB ID: retro_dnov_426

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4604:43688..44216(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19orf40
• Ensembl ID: ENSDNOG00000014134
• Aliases: None
• Description: chromosome 19 open reading frame 40 [Source:HGNC Symbol;Acc:28467]

Sequence

>retro_dnov_426
GAACTCAGTTTTGAGAATGGCCTGACACTGGTAAATTCTCACTCGCCTCGCAGATCCTGCATTCTTTATATCACCAAGGC
TGATGCAGTGGCAGGAAATGGCTAGAGAAAGAGGCTGTGCAGGTGTAAAAACGGCAGGAATCTTCAAGGGATTGCAGCGG
TTGTAAAAACGCAGAGCACGGAACCATCCTGCTCAGCACTAGAGAAGGCTGCCAGGCTGGACCTTGGGATGGTGTCGCTT
CCTGTGGCAAGGCAGATAGAAGCGTCCTGCCTCATTATCCAGTTCATCCAGGAACAAACCAAGAAGCTGAGTAAGAGCCC
TGTCCTCAGAAGAACCAGGCCTGCTCGCCGAGCCGTCCCTCCTTCCAACTGCGCGCAGATCCCAGGAGTGGGAAAAGCTG
AGTCCAGCCCTGCTTCTGCTTCAGAAGTTCCCAAGCACCCAACCGCTAAGGAGCGCGTCCATCCAACGACGCGAGCAGCT
GGGGACACAGCAGCACAGCAAAGTCACGCACTTTTCACCCAGGCCCGG

Alignment

ORF - retro_dnov_426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.91 %
• Parental protein coverage: 82.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLTFEDGLTPVDFHLSNRSCVLYITEADLVAGNAYRKRLVRVRNASNLQGIVLVEKTQMSEQYFPAVQKF
          .L.FE.GLT.V..H...RSC.LYIT.AD.VAGN..RKRL.R..N..NLQGI..V.KTQ..E....A..K.
Retrocopy ELSFENGLTLVNSHSPRRSCILYITKADAVAGNG*RKRLCRCKNGRNLQGIAAVVKTQSTEPSCSALEKA

Parental  TVLDLGMVLLPVASQVEAACLIVQLVQEQTKEHSKNPFLR-KKRA-LLSEPSLLRTVQQIPGVGKVK-AP
          ..LDLGMV.LPVA.Q.EA.CLI.Q..QEQTK..SK.P.LR.K..A.LL.EPSLL.T........K...A.
Retrocopy ARLDLGMVSLPVARQIEASCLIIQFIQEQTKKLSKSPVLR<KNQA<LLAEPSLLPTARRSQEWEKLSPAL

Parental  LLLQKFPSIQQLSNASIQELEQVVGQ-AAAQQIYVFFTQSR
          LLLQKFPS.Q.L..ASIQ..EQ...Q.AA.QQ....FTQ.R
Retrocopy LLLQKFPSTQPLRSASIQRREQLGTQ<AA-QQSHALFTQAR

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	5.64 RPM
SRP012922_cerebellum	0.00 RPM	6.74 RPM
SRP012922_heart	0.00 RPM	0.46 RPM
SRP012922_kidney	0.00 RPM	2.74 RPM
SRP012922_liver	0.00 RPM	2.17 RPM
SRP012922_lung	0.00 RPM	3.36 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.87 RPM
SRP012922_spleen	0.00 RPM	6.98 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_426 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000728	2 retrocopies	retro_cjac_1011, retro_cjac_3952,
Cavia porcellus	ENSCPOG00000011965	1 retrocopy	retro_cpor_1536,
Dasypus novemcinctus	ENSDNOG00000014134	4 retrocopies	retro_dnov_1817, retro_dnov_2382, retro_dnov_426 , retro_dnov_942,
Echinops telfairi	ENSETEG00000002716	1 retrocopy	retro_etel_458,
Loxodonta africana	ENSLAFG00000006401	4 retrocopies	retro_lafr_165, retro_lafr_365, retro_lafr_415, retro_lafr_789,
Myotis lucifugus	ENSMLUG00000013287	1 retrocopy	retro_mluc_522,
Macaca mulatta	ENSMMUG00000017939	1 retrocopy	retro_mmul_788,
Procavia capensis	ENSPCAG00000009727	1 retrocopy	retro_pcap_444,
Sarcophilus harrisii	ENSSHAG00000016372	1 retrocopy	retro_shar_299,