RetrogeneDB ID: retro_dnov_2327

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_64248:1579..1878(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf45
• Ensembl ID: ENSDNOG00000017235
• Aliases: None
• Description: chromosome 12 open reading frame 45 [Source:HGNC Symbol;Acc:28628]

Sequence

>retro_dnov_2327
CTGCTCGGGGGTGTCGGAGTCCAAAGAGCTGCTGACAGCGGGTTCCTCATCAACTCCAAACCTAAGTCCAGAAAGAATTC
CACTCTTCAAACAATTCGGGTAGAAAGGAGCCCCTTATTGGGCCAAGCACATGGCCCAGATGCTCGTCTCACATGGAGGG
CCCAGGCTAATGAAAAACCAAGAACAGAAACGCGAACTGCACAGCCGGGTCGTTTCCATATTGAAAATGTTGATTGACTC
TTGGAAAGGTAATGCAAATGGATGTGGCCTTATTGGAGATGAATCAGTCCCATTCAAAA

Alignment

ORF - retro_dnov_2327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.41 %
• Parental protein coverage: 52.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTAGSGGGRGILDRLLINS---SQKNSTLQTVRVGRSPLLDQVQ---TFLPQMAQANERLRKEMATAPPG
          L..G.G..R......LINS...S.KNSTLQT.RV.RSPLL.Q.......L...AQANE..R.E..TA.PG
Retrocopy LLGGVGVQRAADSGFLINSKPKSRKNSTLQTIRVERSPLLGQAHGPDARLTWRAQANEKPRTETRTAQPG

Parental  RFDIENVD-GTLGKVIQMDVALFEMNQSDPK
          RF.IENVD..TLGKV.QMDVAL.EMNQS..K
Retrocopy RFHIENVD<LTLGKVMQMDVALLEMNQSHSK

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	23.34 RPM
SRP012922_cerebellum	0.41 RPM	10.45 RPM
SRP012922_heart	0.00 RPM	7.66 RPM
SRP012922_kidney	0.00 RPM	17.80 RPM
SRP012922_liver	0.00 RPM	26.78 RPM
SRP012922_lung	0.00 RPM	15.43 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.81 RPM
SRP012922_spleen	0.00 RPM	13.74 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_2327 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014728	1 retrocopy	retro_cjac_333,
Dasypus novemcinctus	ENSDNOG00000017235	1 retrocopy	retro_dnov_2327 ,
Homo sapiens	ENSG00000151131	1 retrocopy	retro_hsap_292,
Gallus gallus	ENSGALG00000012694	1 retrocopy	retro_ggal_15,
Gorilla gorilla	ENSGGOG00000027272	1 retrocopy	retro_ggor_331,
Macaca mulatta	ENSMMUG00000017133	1 retrocopy	retro_mmul_551,
Nomascus leucogenys	ENSNLEG00000006584	1 retrocopy	retro_nleu_2414,
Pongo abelii	ENSPPYG00000004897	1 retrocopy	retro_pabe_382,
Pan troglodytes	ENSPTRG00000005381	1 retrocopy	retro_ptro_240,
Sus scrofa	ENSSSCG00000027792	2 retrocopies	retro_sscr_105, retro_sscr_153,
Tursiops truncatus	ENSTTRG00000005714	1 retrocopy	retro_ttru_1381,