RetrogeneDB ID: retro_dnov_545

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_598:89491..89889(+)
• Located in intron of: ENSDNOG00000007641

Retrocopy information

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

Parental gene information

• Parental gene symbol: STMN2
• Ensembl ID: ENSDNOG00000003373
• Aliases: None
• Description: stathmin-like 2 [Source:HGNC Symbol;Acc:10577]

Sequence

>retro_dnov_545
GATATCCAGGTCAAAGAACTGGAGAAGCGTGCCTCAGGCCAGGCCTTTGAGCTGATACTCAGCCCTCGGTCAAAAGAATC
TGTCCCAGAATTTCCCTTTTCCCCTCCAAAGAAGGATCTTTCCCTGGAGGAAATTTAGAAGAAGTTAGAAGCTGCAGAAG
AAAGACGCAAGTCCCATGAAGCTGAGGTCTTGAAGCAGCTTGCTGAGAAACGAGAGCATGAGAAAGAAGTGCTTCAGAAA
GCAATAAAGAAAACAACAACTTCAGTAAAATGGCGGAAGAGAAATTGACCCACAAAATGGAAGCCAACAAAGAGAACCAA
GAGGCACAAATGGCTGCCAAACTGGAACGTTTGCGAGAAAAGGACAAGCACATTGAAGAAGTACAGAAGAACAAAGAA

Alignment

ORF - retro_dnov_545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.11 %
• Parental protein coverage: 74.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DMEVKQINKRASGQAFELILKPPSPISEAPRTLASPKKKDLSLEEIQKKLEAAEERRKSQEAQVLKQLAE
          D..VK...KRASGQAFELIL.P.S..S..P....SP.KKDLSLEEI.KKLEAAEERRKS.EA.VLKQLAE
Retrocopy DIQVKELEKRASGQAFELILSPRSKES-VPEFPFSPPKKDLSLEEI*KKLEAAEERRKSHEAEVLKQLAE

Parental  KREHEREVLQKAL-EENNNFSKMAEEKLILKMEQIKENREANLAAIIERLQEKERHAAEVRRNKE
          KREHE.EVLQKA...ENNNFSKMAEEKL..KME..KEN.EA..AA..ERL.EK..H..EV..NKE
Retrocopy KREHEKEVLQKAI<KENNNFSKMAEEKLTHKMEANKENQEAQMAAKLERLREKDKHIEEVQKNKE

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	13.03 RPM	26.06 RPM
SRP012922_cerebellum	21.86 RPM	399.90 RPM
SRP012922_heart	2.09 RPM	0.93 RPM
SRP012922_kidney	6.57 RPM	1.10 RPM
SRP012922_liver	1.55 RPM	28.17 RPM
SRP012922_lung	9.16 RPM	15.73 RPM
SRP012922_quadricep_muscle	0.35 RPM	0.52 RPM
SRP012922_spleen	9.16 RPM	88.82 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_545 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003373	3 retrocopies	retro_dnov_2381, retro_dnov_545 , retro_dnov_831,
Dasypus novemcinctus	ENSDNOG00000003756	1 retrocopy	retro_dnov_935,
Mustela putorius furo	ENSMPUG00000001863	1 retrocopy	retro_mputfur_68,
Otolemur garnettii	ENSOGAG00000027869	2 retrocopies	retro_ogar_2664, retro_ogar_330,
Oryzias latipes	ENSORLG00000008251	1 retrocopy	retro_olat_37,
Sorex araneus	ENSSARG00000010989	1 retrocopy	retro_sara_756,
Ictidomys tridecemlineatus	ENSSTOG00000025094	2 retrocopies	retro_itri_1012, retro_itri_1423,
Tarsius syrichta	ENSTSYG00000014759	1 retrocopy	retro_tsyr_26,