RetrogeneDB ID: retro_dnov_1081

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_14404:50312..50771(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000004225
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SKA1
• Ensembl ID: ENSDNOG00000000190
• Aliases: None
• Description: spindle and kinetochore associated complex subunit 1 [Source:HGNC Symbol;Acc:28109]

Sequence

>retro_dnov_1081
ATTAAGAAATCAGATCTTAATCGTGAGGAACCAGTCAAAGTTGAGGAGACTGCAACCACAAAGAATTCTCCCAAAAGAAC
AAAGAAATATTAAAGAAATTCCATTTATAACTTCTGATGAGTTCAATGGTGCTCCTACATGCATGAAAACCCACTTAACC
TATTGCCAAATTAATGATGTTATTAAAGAAATCAACAAGGCAATAATAAATAAATATAAACTCCTACATCAACCAAAAAA
GTCTATGAGTTCTGTGGCCAGAAATCTCTTCCACAGATTTATTGATGAAGAAACAAAGAATACTAAAGGTCATTGTTTTA
TAGTGGAAGCTGCTGGCATAAAAGAGTTCTCAGCTTTGAAAGTTGAAAAGAAGTTTCACACGGAATGCTGAATATTTTAT
GGCACTGCCAGAGGCTATCAGAGATCCAAGGGCAGGGACTCATTCATTATGTTATAAAC

Alignment

ORF - retro_dnov_1081 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.19 %
• Parental protein coverage: 59.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VKESELNPEELVKVEETAPTKK-LLKEQRNIKE-PFITSDEFNGXXXYMKSRLTYCQINDVIKEINKAVI
          .K.S.LN.EE.VKVEETA.TK..L.KEQRNIKE.PFITSDEFNG....MK..LTYCQINDVIKEINKA.I
Retrocopy IKKSDLNREEPVKVEETATTKN>LPKEQRNIKEIPFITSDEFNGAPTCMKTHLTYCQINDVIKEINKAII

Parental  SKYKILHQPKKSMNSVARNLYHRFIDEETKDTKGHYFIVEA-DIKEFTSL-KVDKKF-HGMLNILRHCRR
          .KYK.LHQPKKSM.SVARNL.HRFIDEETK.TKGH.FIVEA..IKEF..L.K....F.HGMLNIL.HC.R
Retrocopy NKYKLLHQPKKSMSSVARNLFHRFIDEETKNTKGHCFIVEAAGIKEFSAL>KLKRSF>HGMLNILWHCQR

Parental  ISEIRGQGLTRYAIN
          .SEI.GQGL..Y.IN
Retrocopy LSEIQGQGLIHYVIN

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	2.72 RPM
SRP012922_cerebellum	0.00 RPM	0.14 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.00 RPM
SRP012922_liver	0.00 RPM	0.15 RPM
SRP012922_lung	0.00 RPM	0.31 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	7.44 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_1081 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008555	2 retrocopies	retro_cjac_1103, retro_cjac_875,
Dasypus novemcinctus	ENSDNOG00000000190	1 retrocopy	retro_dnov_1081 ,
Loxodonta africana	ENSLAFG00000005238	1 retrocopy	retro_lafr_849,
Myotis lucifugus	ENSMLUG00000013388	1 retrocopy	retro_mluc_2127,
Sus scrofa	ENSSSCG00000004518	1 retrocopy	retro_sscr_360,
Tursiops truncatus	ENSTTRG00000015539	1 retrocopy	retro_ttru_1083,