RetrogeneDB ID: retro_dnov_2141

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_50857:11090..11518(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN33
• Ensembl ID: ENSDNOG00000007532
• Aliases: None
• Description: tetraspanin 33 [Source:HGNC Symbol;Acc:28743]

Sequence

>retro_dnov_2141
CTGCTCTTCTTCAACTTGCTCTCCTGGGTGATTTCCATGGTGATGGTGGCTGTGGGAGTCTATGACCGGCTGATGAGGCA
CGCAGTAGCCTTGGCCTGCCTGGTGGTGGACCCTGCCATCCTGCTGGGCGGCCTTATGTCCCTGCTCACCTTTTGTGGCT
GCATTGGATCCCTCTGTGAGAACATCTGCCTCCTTCAGAAGTTCTCCCTCTGCCTCACCGTCGTGCTCCTGCTGCACCTG
GCTGCTGGAGTTCTGGGTTTTGTCTTCTCAGGCAGGGTTGGGGCAAAGTGAGCGAGATCATCAACAATGCCATGGTACAC
TACCGAGATGACTTAGATCTGCAGAATCTCATTGGCTTTGGCCAGAAGTTCAGCTGCTGTGGAGGGATTTCCTACAGGGA
CTGGTCCCTGAACATGTACTTCAACTGT

Alignment

ORF - retro_dnov_2141 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.52 %
• Parental protein coverage: 57.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFFLNMLFWVIAMLMMAVGVYARLMKHAEAAFACLAVDPAILLIVVGVLMFLLTFCGCIGSLRENICLLQ
          L.F.N.L.WVI.M.M.AVGVY.RLM.HA..A.ACL.VDPAILL...G.LM.LLTFCGCIGSL.ENICLLQ
Retrocopy LLFFNLLSWVISMVMVAVGVYDRLMRHA-VALACLVVDPAILL---GGLMSLLTFCGCIGSLCENICLLQ

Parental  TFSICLTVVFLLQLAAGVLGFVFSDKAR-GKVSEIINNAIVHYRDDLDLQNLIDFGQKKFSCCGGISYRD
          .FS.CLTVV.LL.LAAGVLGFVFS.....GKVSEIINNA.VHYRDDLDLQNLI.FGQ.KFSCCGGISYRD
Retrocopy KFSLCLTVVLLLHLAAGVLGFVFSGRVG<GKVSEIINNAMVHYRDDLDLQNLIGFGQ-KFSCCGGISYRD

Parental  W-LNMYFNC
          W.LNMYFNC
Retrocopy WSLNMYFNC

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	0.19 RPM	7.78 RPM
SRP012922_cerebellum	0.41 RPM	13.33 RPM
SRP012922_heart	0.46 RPM	3.71 RPM
SRP012922_kidney	0.00 RPM	19.17 RPM
SRP012922_liver	0.31 RPM	2.32 RPM
SRP012922_lung	0.15 RPM	3.51 RPM
SRP012922_quadricep_muscle	0.69 RPM	29.94 RPM
SRP012922_spleen	4.69 RPM	152.00 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_2141 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
Bos taurus	ENSBTAG00000007253	1 retrocopy	retro_btau_683,
Dasypus novemcinctus	ENSDNOG00000007532	1 retrocopy	retro_dnov_2141 ,
Dasypus novemcinctus	ENSDNOG00000012685	1 retrocopy	retro_dnov_91,