RetrogeneDB ID: retro_dnov_2445

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_75405:7525..7824(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSCB
• Ensembl ID: ENSDNOG00000011178
• Aliases: None
• Description: HscB iron-sulfur cluster co-chaperone homolog (E. coli) [Source:HGNC Symbol;Acc:28913]

Sequence

>retro_dnov_2445
AACTATTCCATCAGATTTGACCTCAAGAAGCTCCAGCAAAAGTGCCAGAAATCACAGCATTTTGTCCACCCAGATTTCTC
CAGCCAGAGGTCTCAGCCTGAAAAGGACTTCTCAGAGCGGCATTCAGTCTGAGCAATGATGCCTATAGGACTCTTCTAGT
TGCCCTGAGCAGGAGAAGATACCTTGTAAGTAAGTTAAAGCTCTGTGAAACAGAGATTTGAGAAGGAACGTATTATGAAA
AGGACAGCAAATTTCTCATAGAAATAGTGGAAATCAATGAAAAACTTGCAGAAGCTCAA

Alignment

ORF - retro_dnov_2445 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.36 %
• Parental protein coverage: 62.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NCSFIVDTAKLQHRYQKLQRLVHPDFFSQRSQTEKDFSEKHS-RLVNDAYKTLLAPLSRGLYL---LKLH
          N.S...D..KLQ...QK.Q..VHPDF.SQRSQ.EKDFSE.HS..L.NDAY.TLL..LSR..YL...LKL.
Retrocopy NYSIRFDLKKLQQKCQKSQHFVHPDFSSQRSQPEKDFSERHS<SLSNDAYRTLLVALSRRRYLVSKLKLC

Parental  GIEIHEGTDYEMDREFLMEIMEINEKLAEAQ
          ..EI.EGT.YE.D..FL.EI.EINEKLAEAQ
Retrocopy ETEI*EGTYYEKDSKFLIEIVEINEKLAEAQ

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	6.81 RPM
SRP012922_cerebellum	0.00 RPM	3.02 RPM
SRP012922_heart	0.00 RPM	3.71 RPM
SRP012922_kidney	0.00 RPM	12.32 RPM
SRP012922_liver	0.00 RPM	7.43 RPM
SRP012922_lung	0.00 RPM	5.35 RPM
SRP012922_quadricep_muscle	0.00 RPM	4.67 RPM
SRP012922_spleen	0.00 RPM	5.95 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_2445 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011178	2 retrocopies	retro_dnov_2445 , retro_dnov_851,
Ictidomys tridecemlineatus	ENSSTOG00000011587	1 retrocopy	retro_itri_797,