RetrogeneDB ID: retro_dnov_2642

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_93649:116..871(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000016043
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEC61A1
• Ensembl ID: ENSDNOG00000015763
• Aliases: None
• Description: Sec61 alpha 1 subunit (S. cerevisiae) [Source:HGNC Symbol;Acc:18276]

Sequence

>retro_dnov_2642
GACAAAGCCCGAGCTTTACGGGAAGCTTTCTATCGCCAGAATTTACCCAATCTCATGAACCTCACTGCTACAGTTTTCGT
GTTTGCTGTTGTTATATATTTTCAGGGATTTCACGAGGACTTGCCCATTAAGTCGGCCTGGTACAAAGGACAGTACAGCA
GCTACACCATCAAGCTCTTCTACACCTCCTATATTCCCATCATTCTCCAGTCGGCCTTGGTGTCCAACCTCTATGTTATT
TCTCAGATGCTGTCTGTGCGATTTAGTGGCAACTTCTAGAAAATTTACTGGGACAGTGGGCTGATGTCCGTGCGGATGGA
CCTGCTTGTTCTTACCCTGTTGGAGACCTTTATTATTATCTTTCTCCTCCTGAGTCCAGGGGTGCCATTTTTGAGGATCC
TGTCCATGTAGTTGTTTATATCATCTTCAGGCTGGGATCATGTGCATTCTTCTCAGAGACGTGGATAGAGGTGTCTGGTT
CCTCAGCCAAAGATGTAGCTAAACAGTTTAAAGTACAGCAAATGGTAATGAGGGGTCACAGAGATATCTCTATGGTTCAG
GAGCTTACTAGGTATATCCCCAGAGCAGCTGCATTTGGTGGCCTGTGCATCAGTGCCCTGTCGGTGCTGGTGGAATTGCT
GGGGGTCATGGGCTCTGGCACTGGAATTCTACTTGCAGTCACTATTATTTATCAGTATTTTGAAATATTTGTTAAGGAAC
AGGCCGAGGTTGGTGGGATGGGTGCTTTGTTTTTT

Alignment

ORF - retro_dnov_2642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 52.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DKVRALREAFYRQNLPNLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQ
          DK.RALREAFYRQNLPNLMNL.AT.FVFAVVIYFQGF..DLPIKSA.Y.GQY..Y.IKLFYTS.IPIILQ
Retrocopy DKARALREAFYRQNLPNLMNLTATVFVFAVVIYFQGFHEDLPIKSAWYKGQYSSYTIKLFYTSYIPIILQ

Parental  SALVSNLYVISQMLSARFSGN-LLVSLLGTWSDTSSGGPARAYPVGGLCYYLSPPESFGSVLEDPVHAVV
          SALVSNLYVISQMLS.RFSGN.LL..LLG.W.D....GPA..YPVG.L.YYLSPPES.G...EDPVH.VV
Retrocopy SALVSNLYVISQMLSVRFSGN<LLENLLGQWADVRADGPACSYPVGDLYYYLSPPESRGAIFEDPVHVVV

Parental  YIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRETSMVHELNRYIPTAAAFGGLCIGALSV
          YI.F.LGSCAFFS.TWIEVSGSSAKDVAKQ.K.QQMVMRGHR..SMV.EL.RYIP.AAAFGGLCI.ALSV
Retrocopy YIIFRLGSCAFFSETWIEVSGSSAKDVAKQFKVQQMVMRGHRDISMVQELTRYIPRAAAFGGLCISALSV

Parental  LADFLSAIESSTRILLAVTIIYQYFEIFVKEQSEVSSIGALLF
          L...L....S.T.ILLAVTIIYQYFEIFVKEQ.EV...GAL.F
Retrocopy LVELLGVMGSGTGILLAVTIIYQYFEIFVKEQAEVGGMGALFF

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	0.58 RPM	121.93 RPM
SRP012922_cerebellum	2.20 RPM	24.74 RPM
SRP012922_heart	0.93 RPM	6.73 RPM
SRP012922_kidney	0.27 RPM	41.07 RPM
SRP012922_liver	0.15 RPM	93.97 RPM
SRP012922_lung	1.07 RPM	65.21 RPM
SRP012922_quadricep_muscle	1.04 RPM	6.75 RPM
SRP012922_spleen	0.80 RPM	93.29 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_2642 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015763	1 retrocopy	retro_dnov_2642 ,
Sarcophilus harrisii	ENSSHAG00000013915	1 retrocopy	retro_shar_641,