RetrogeneDB ID: retro_dnov_91

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1437:399967..400480(+)
• Located in intron of: ENSDNOG00000024528

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN5
• Ensembl ID: ENSDNOG00000012685
• Aliases: None
• Description: tetraspanin 5 [Source:HGNC Symbol;Acc:17753]

Sequence

>retro_dnov_91
TTCTCTGTGTTCCTCAGCCTCATCTTCTTCCTGGAAGTGGCTACTGGGATCCTGGCCTTCATATTCAAGGACTGGATATG
CGACCAGCTCAACCTCTTCATCAACAATAATGTCAAGGTCTATAAGGATGATATTGACCTCCAGAACCTCACTGACTTTC
CTCAGCAATACTGGTCTTGGTGTGGAGCCCGAGGGCCCAATGACTGGATCCTCAATATCTACTTCAACTGCACTGACTTG
AAACCGAGCCAGGAGCACTGTGGGGTGCCCTTCTACTACATCCAGGACCCCATGGAAGATGTCCTCAACACCCATTATGG
TTATCATATTCTACCCAAACTGGAGCTGGAGCAGCCAGACTCCATCTACACCAAGGGCTGTGTGGACCAGTTTGAGAAGT
GGCTGCAGGACATGGTGGCTAGGTTCTTTGTGGGCATCAACTTCCTCCAGATCTTTGGCATCTGCACAGCCCAGAACCTC
ATGAATGACATCCAGGCAGTAAAGGCCAACTGG

Alignment

ORF - retro_dnov_91 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.0 %
• Parental protein coverage: 72.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FSVFLGIIFFLELTAGVLAFVFKDWIKDQLYFFINNNIRAYRDDIDLQNLIDFTQEYWQCCGAFGADDWN
          FSVFL..IFFLE...G.LAF.FKDWI.DQL..FINNN...Y.DDIDLQNL.DF.Q.YW..CGA.G..DW.
Retrocopy FSVFLSLIFFLEVATGILAFIFKDWICDQLNLFINNNVKVYKDDIDLQNLTDFPQQYWSWCGARGPNDWI

Parental  LNIYFNCTDSNASRERCGVPFSCCTKDPAEDVINTQCGYDARQKPEVDQQIVIYTKGCVPQFEKWLQDNL
          LNIYFNCTD...S.E.CGVPF.....DP.EDV.NT..GY....K.E..Q...IYTKGCV.QFEKWLQD..
Retrocopy LNIYFNCTDLKPSQEHCGVPF-YYIQDPMEDVLNTHYGYHILPKLELEQPDSIYTKGCVDQFEKWLQD--

Parental  TIVAGIFIGIALLQIFGICLAQNLVSDIEAVRASW
          ..VA..F.GI..LQIFGIC.AQNL..DI.AV.A.W
Retrocopy -MVARFFVGINFLQIFGICTAQNLMNDIQAVKANW

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	2.92 RPM
SRP012922_cerebellum	0.00 RPM	16.63 RPM
SRP012922_heart	0.00 RPM	0.93 RPM
SRP012922_kidney	0.00 RPM	4.93 RPM
SRP012922_liver	0.00 RPM	0.77 RPM
SRP012922_lung	0.61 RPM	4.73 RPM
SRP012922_quadricep_muscle	0.17 RPM	0.87 RPM
SRP012922_spleen	0.23 RPM	10.76 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_91 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013851	1 retrocopy	retro_amel_742,
Canis familiaris	ENSCAFG00000010287	1 retrocopy	retro_cfam_314,
Choloepus hoffmanni	ENSCHOG00000013549	1 retrocopy	retro_chof_2337,
Dasypus novemcinctus	ENSDNOG00000007532	1 retrocopy	retro_dnov_2141,
Dasypus novemcinctus	ENSDNOG00000012685	1 retrocopy	retro_dnov_91 ,
Echinops telfairi	ENSETEG00000007405	1 retrocopy	retro_etel_1985,
Pteropus vampyrus	ENSPVAG00000003024	1 retrocopy	retro_pvam_79,