RetrogeneDB ID: retro_dnov_2496

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_80345:6081..6609(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STOM
• Ensembl ID: ENSDNOG00000015723
• Aliases: None
• Description: stomatin [Source:HGNC Symbol;Acc:3383]

Sequence

>retro_dnov_2496
ATGGCTGAGAAGTGGCAGGCAGTGGACACCCAAGCCCAGCGGCTCCCCGACTCCTTCAAAGATAGCCCCAATATAGGCCT
TGGGCCTTGTGGATGGATTTTGGTGGCTGCTGTCTCATTCTTATTCATGGTTATAACTTTCCCCATATCGATATGGATGT
GTATAAAGATCATCAAAGAGTATGAAAGAGCGATCATCTTTAGACTAGGACACATTTTACAAGGAGGAGCCAAAGGACCT
GGTTTGTTTTTTATTCTGCCATGCACTGACAACTTCATCAAAGTGTACATGAGAACTATTTCATTTGATATTCCTCCTCA
GGAGATCCTCACCAAGGACTCAGTGACAATTAGTGTGGATGGAATTGTCTATTACCATGTGCAGAATGCAACCCTGGCTG
TGGCAAATATCACCAATGCTGACTCAGCAACTCTTCTTTTGGCTTAGACTATGCTGAGGAATGTTCTGGGCACCAAGAAC
CTTTCTCAGATCCTCTCTGACAGAGAAGAAATTGCACATAACATGCAG

Alignment

ORF - retro_dnov_2496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.05 %
• Parental protein coverage: 60.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEKRQGADTQARRLPDSFKDSPNTGLGPCGWILVA-VSFLFTVITFPISIWMCIKIIKEYERAIIFRLG
          MAEK.Q..DTQA.RLPDSFKDSPN.GLGPCGWILVA.VSFLF.VITFPISIWMCIKIIKEYERAIIFRLG
Retrocopy MAEKWQAVDTQAQRLPDSFKDSPNIGLGPCGWILVAAVSFLFMVITFPISIWMCIKIIKEYERAIIFRLG

Parental  RILQGGAKGPGLFFILPCTDNFIKVDMRTISFDIPPQEILTKDSVTISVDGVVYYRVQNATLAVANITNA
          .ILQGGAKGPGLFFILPCTDNFIKV.MRTISFDIPPQEILTKDSVTISVDG.VYY.VQNATLAVANITNA
Retrocopy HILQGGAKGPGLFFILPCTDNFIKVYMRTISFDIPPQEILTKDSVTISVDGIVYYHVQNATLAVANITNA

Parental  DSATRLLAQTTLRNVLGTKNLSQILSDREEIAHNMQ
          DSAT.LLA.T.LRNVLGTKNLSQILSDREEIAHNMQ
Retrocopy DSATLLLA*TMLRNVLGTKNLSQILSDREEIAHNMQ

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	15.17 RPM	82.07 RPM
SRP012922_cerebellum	0.27 RPM	1.92 RPM
SRP012922_heart	2.09 RPM	9.75 RPM
SRP012922_kidney	3.56 RPM	15.61 RPM
SRP012922_liver	10.22 RPM	57.59 RPM
SRP012922_lung	7.18 RPM	55.29 RPM
SRP012922_quadricep_muscle	1.21 RPM	5.71 RPM
SRP012922_spleen	10.30 RPM	61.81 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_2496 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	ENSDNOG00000015723	1 retrocopy	retro_dnov_2496 ,
Nomascus leucogenys	ENSNLEG00000017145	1 retrocopy	retro_nleu_647,
Otolemur garnettii	ENSOGAG00000002879	2 retrocopies	retro_ogar_2886, retro_ogar_291,
Oreochromis niloticus	ENSONIG00000013021	1 retrocopy	retro_onil_33,