RetrogeneDB ID: retro_dnov_863

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_11533:62370..62968(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000014426
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CALU
• Ensembl ID: ENSDNOG00000010477
• Aliases: None
• Description: calumenin [Source:HGNC Symbol;Acc:1458]

Sequence

>retro_dnov_863
CCATCGGTGCGCAAGGAACGAGAGGTGGCGCTCGACTCGTAGTTCCGGAATCGAACTCCCGAAGACAATCAGAGCTTCCA
GTAAGACCAAATAGTCTTTCCTGGGTAAAGAGGACTTCAAGACTATAGATCAGCTCATCCCAGATGAGAGCAAGGAGAGG
CTGGGGATGATTGTCAATCGAATCGACAGTGATGGAGGTGGCTTGGTCACCACCTAGGAACTGAGAACAGGGATCAATCG
GGTGCAGAAAAGATACATCTATGACAATGTCGCTGAAGTGTGGAAGGATTATGATCGGGACAAAGACGATACGATTTCCT
GGAAAGAATACAAACAAGTCACCTATGGATACTATCTAGGAAACCCCGAAGAGTTTCATGATACTTCAGATCATCAAACC
TTCAAAAAGATGCTTCCACGTGACGAGAGAAGGTTCAAGGCTGCAGAGCTCAAAGGTGACCAGACGGCCACTCGGGAGGA
GTTCACAGCCTTTCTGCACCCTGAGGAGTTCGAGCATATGAAGGAAATCGTGGTTTTGGAAACTCTGGAGGACATCGACA
AGAACGGGGAGGGCTTCGTGGATGAGGATGACTATATT

Alignment

ORF - retro_dnov_863 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51. %
• Parental protein coverage: 90.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PTEKKDR-VHHEPQLSDKVHDDAQSFDYDHD-AFLGAEEAKTFDQLTPEESKERLGKIVSKIDGDKDGFV
          P...K.R.V............D.QSF..D....FLG.E..KT.DQL.P.ESKERLG.IV..ID.D..G.V
Retrocopy PSVRKEREVALDS*FRNRTPEDNQSFQ*DQI>SFLGKEDFKTIDQLIPDESKERLGMIVNRIDSDGGGLV

Parental  TVDELKDWIKFAQKRWIYEDVERQWKGHDLNEDGLVSWEEYKNATYGYVLDDPD----PDDGFNYKQMMV
          T..EL...I...QKR.IY..V...WK..D...D...SW.EYK..TYGY.L..P.......D....K.M..
Retrocopy TT*ELRTGINRVQKRYIYDNVAEVWKDYDRDKDDTISWKEYKQVTYGYYLGNPEEFHDTSDHQTFKKMLP

Parental  RDERRFKMADKDGDLIATKEEFTAFLHPEEYDYMKDIVVQETMEDIDKNADGFIDLEEYI
          RDERRFK.A...GD..AT.EEFTAFLHPEE...MK.IVV.ET.EDIDKN..GF.D...YI
Retrocopy RDERRFKAAELKGDQTATREEFTAFLHPEEFEHMKEIVVLETLEDIDKNGEGFVDEDDYI

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	10.89 RPM	26.84 RPM
SRP012922_cerebellum	19.66 RPM	7.84 RPM
SRP012922_heart	6.96 RPM	9.28 RPM
SRP012922_kidney	4.11 RPM	8.21 RPM
SRP012922_liver	7.43 RPM	16.56 RPM
SRP012922_lung	20.62 RPM	25.96 RPM
SRP012922_quadricep_muscle	3.63 RPM	11.25 RPM
SRP012922_spleen	23.69 RPM	30.68 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_863 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010477	1 retrocopy	retro_dnov_863 ,
Pongo abelii	ENSPPYG00000017982	1 retrocopy	retro_pabe_211,
Pan troglodytes	ENSPTRG00000019668	1 retrocopy	retro_ptro_6,