RetrogeneDB ID: retro_dnov_977

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_12907:66479..67196(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPP1
• Ensembl ID: ENSDNOG00000004231
• Aliases: None
• Description: membrane protein, palmitoylated 1, 55kDa [Source:HGNC Symbol;Acc:7219]

Sequence

>retro_dnov_977
CGAGTGGCGAGTGTGGCCCAATCTGCTCCGAGTGAAGCCCCAAGCTGTAGTCCCTTTGAGAAGAAGAAGAAGTACAAAGA
CAAGTATCTGGCAAAACACAGCTCCATTTTTGACCAATTGAATGTTTCCTATGAGGAAGTTGTCCGGCTCCCTGCGTTCA
AGAGGAAGACCCTGGTGCTGATAGGAGCCAGTGGGGTGGGTCGTAGCCACATAAAGAATGCCCTGCTCAGCCAGAATCCA
GAGAAGTTTGTGTACCCCACCCCGTATACGACCCGGCTCCCAAAGAAGAGCGAGGAGGATGGGAAGGAGTACCACTTCAT
CTCAACTGAGGAGATGACAAGGAACATCTCTGCCAATGAGTTCTTGGAGTTTGGCAGCTACCAGGACAACATGTTTGGCA
CCAAATTTGAAACAGTGCATGAGATTCATAGGCAGGACAAAATTGCCATCCTTGACATTGAGCCCCAGACCCTGAAGATT
GTTCGGACAGCAGAACTTTCACCTTTCGTTGTGTTCATTGCACCTACTGACCAGGGCACTCAGATGGAAGCCCTGCAGCA
GCTGCAGAAGGACTCTGAGGCCTTCCGCAGCCAGTCCACACACTACTTTGACCTCTCCTTGGTTAATAATGGCCTTGATG
AAACTCTCAAGAAATTGCAAGAAGCCTTTGATCAGGCACGCAGTTCTCCACAGTGAGGGCCTGTCTCCTGGGTTTAC

Alignment

ORF - retro_dnov_977 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 73.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVASVAQSAPSEAPSCXXXXXXXXXXXXXXXXXXXXFDQLDVVSYEEVVRLPAFKRKTLVLIGASGVGRS
          RVASVAQSAPSEAPSC....................FDQL..VSYEEVVRLPAFKRKTLVLIGASGVGRS
Retrocopy RVASVAQSAPSEAPSCSPFEKKKKYKDKYLAKHSSIFDQLN-VSYEEVVRLPAFKRKTLVLIGASGVGRS

Parental  HIKNALLSQNPEKFVYPTPYTTRLPKKSEEDGKEYHFISTEEMTRNISANEFLEFGSYQGNMFGTKFETV
          HIKNALLSQNPEKFVYPTPYTTRLPKKSEEDGKEYHFISTEEMTRNISANEFLEFGSYQ.NMFGTKFETV
Retrocopy HIKNALLSQNPEKFVYPTPYTTRLPKKSEEDGKEYHFISTEEMTRNISANEFLEFGSYQDNMFGTKFETV

Parental  HEIHRQDKIAILDIEPQTLKIVRTAELSPFIVFIAPTDQGTQTEALQQLQKDSEAIRSQYAHYFDLSLVN
          HEIHRQDKIAILDIEPQTLKIVRTAELSPF.VFIAPTDQGTQ.EALQQLQKDSEA.RSQ..HYFDLSLVN
Retrocopy HEIHRQDKIAILDIEPQTLKIVRTAELSPFVVFIAPTDQGTQMEALQQLQKDSEAFRSQSTHYFDLSLVN

Parental  NGVDETLKKLQEAFDQACSSPQWVPVSWVY
          NG.DETLKKLQEAFDQA.SSPQ..PVSWVY
Retrocopy NGLDETLKKLQEAFDQARSSPQ*GPVSWVY

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	21.78 RPM	37.14 RPM
SRP012922_cerebellum	6.32 RPM	9.21 RPM
SRP012922_heart	2.32 RPM	5.34 RPM
SRP012922_kidney	9.04 RPM	19.44 RPM
SRP012922_liver	2.79 RPM	4.49 RPM
SRP012922_lung	4.28 RPM	9.16 RPM
SRP012922_quadricep_muscle	5.02 RPM	10.73 RPM
SRP012922_spleen	34.68 RPM	64.90 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_977 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004231	1 retrocopy	retro_dnov_977 ,
Felis catus	ENSFCAG00000006578	1 retrocopy	retro_fcat_1352,
Pteropus vampyrus	ENSPVAG00000009226	1 retrocopy	retro_pvam_709,
Tupaia belangeri	ENSTBEG00000011524	2 retrocopies	retro_tbel_4481, retro_tbel_564,