RetrogeneDB ID: retro_dnov_641

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_714:214531..215009(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE1
• Ensembl ID: ENSDNOG00000013271
• Aliases: None
• Description: non-SMC element 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29897]

Sequence

>retro_dnov_641
TTGTTTATGTTTAGAAAGATTTTGGAACTGACTTTTTACTTAGAAACTGGCTTTGCCTCTTTCACAAACATTTTGAGACT
GTTTGATCAACTTCAAGGCCAGAAGAAGAGGAAAAAGGAAGCTGAACACATGCTACACAAGTTTGTACAAAACAAATGGC
TGATTGAGAAACAAGGGGAATTCACCCTGCCTTGCTGGGCCATCTTGGAAATGCATCAGTTCATTTAGGAGACCTACTCC
AGTGCTATAAAGATCTGTAACATCTGCCACAGCCTCATGATCCAGGGTCAAAGCTGCAAAACATGTGAGATTTGAATGTA
CTTACCACAAATGGCCAAGTAATTCCAGTCTAATTTTGAATTGGTCTGCCACCACTGTAACATCTATTGGTCCCATGAGG
TAAAGAAATCTTGGACCCTGAGAAGAGGGAGTCTGGTATCTCCAGACTGAATAATAAGTCTTTCAACCCAGGCAACAC

Alignment

ORF - retro_dnov_641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.26 %
• Parental protein coverage: 70.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LDLFRKALDLIIDSETGFASSTNILNLVDQLKGKKMRKKEAEHVLQKFVQNKWLIEKEGEFTLHSRAILE
          L..FRK.L.L....ETGFAS.TNIL.L.DQL.G.K.RKKEAEH.L.KFVQNKWLIEK.GEFTL...AILE
Retrocopy LFMFRKILELTFYLETGFASFTNILRLFDQLQGQKKRKKEAEHMLHKFVQNKWLIEKQGEFTLPCWAILE

Parental  MEQYIRETYPDSVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFKSNSEPRCPHCNDYWPHEI-PEVFD
          M.Q.I.ETY....KICNICHSL.IQGQSC.TC.I.M.LP..AK.F.SN.E..C.HCN.YW.HE...E..D
Retrocopy MHQFI*ETYSSAIKICNICHSLMIQGQSCKTCEI*MYLPQMAK*FQSNFELVCHHCNIYWSHEV<KEILD

Parental  PEKDREAGISRSNKKS-LRSRQH
          PEK.RE.GISR.N.KS....RQH
Retrocopy PEK-RESGISRLNNKS<FQPRQH

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	42.78 RPM
SRP012922_cerebellum	0.00 RPM	66.40 RPM
SRP012922_heart	0.00 RPM	58.70 RPM
SRP012922_kidney	0.00 RPM	94.73 RPM
SRP012922_liver	0.00 RPM	81.12 RPM
SRP012922_lung	0.00 RPM	49.64 RPM
SRP012922_quadricep_muscle	0.00 RPM	21.29 RPM
SRP012922_spleen	0.00 RPM	43.15 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_641 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011003	2 retrocopies	retro_chof_1394, retro_chof_339,
Callithrix jacchus	ENSCJAG00000020515	1 retrocopy	retro_cjac_2191,
Dasypus novemcinctus	ENSDNOG00000013271	1 retrocopy	retro_dnov_641 ,
Mus musculus	ENSMUSG00000030750	2 retrocopies	retro_mmus_1564, retro_mmus_2488,
Ochotona princeps	ENSOPRG00000011452	1 retrocopy	retro_opri_732,