RetrogeneDB ID: retro_dnov_1591

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_24214:5115..5425(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SIVA1
• Ensembl ID: ENSDNOG00000005703
• Aliases: None
• Description: SIVA1, apoptosis-inducing factor [Source:HGNC Symbol;Acc:17712]

Sequence

>retro_dnov_1591
TCCGCACAGCCCGGCCCCATGGAGGTCCTAGGTGTTGTCAGGGGCTGATTAGCTGGAATGGGCATATGGTGCAGAGTCAC
ATCCAGGCCTGCGAAGCCGACCTGTTGGTGGCCGTTTCCAGGACCTGCTCACTGTGCATCCGAAACATGGATGGGAAGGC
GGCATGCAGCCAGCGTGAGCACCCCCTGTGTGGATACTGCCTGCTACCTGCTGAGGCTGCGTTGCCAGGTCCTGATCTTC
CTGTGCCGTAATCAGCTATGGTGACATCCAGGAGAAAGTGCTCTGCCTGGTCTGTACCATATTTGAAGCC

Alignment

ORF - retro_dnov_1591 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.04 %
• Parental protein coverage: 76.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SPQPGPV-GIPGAIRGQLLIGRDGRLVRGSVQACEADPSVAVSRACSSCIRSMDGKAACSQCERPLCGHC
          S.QPGP..G.P....G..LI...G..V....QACEAD..VAVSR.CS.CIR.MDGKAACSQ.E.PLCG.C
Retrocopy SAQPGPM<GGPRCCQG--LISWNGHMVQSHIQACEADLLVAVSRTCSLCIRNMDGKAACSQREHPLCGYC

Parental  L-RTCWGCGAGACSSCAVVDYGDIHEKALCPVCAVFEA
          L..TC.GC.A...SSCAV..YGDI.EK.LC.VC..FEA
Retrocopy L<ATC*GCVARS*SSCAVISYGDIQEKVLCLVCTIFEA

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	18.86 RPM
SRP012922_cerebellum	0.00 RPM	14.71 RPM
SRP012922_heart	0.00 RPM	11.60 RPM
SRP012922_kidney	0.00 RPM	16.43 RPM
SRP012922_liver	0.00 RPM	8.36 RPM
SRP012922_lung	0.00 RPM	33.60 RPM
SRP012922_quadricep_muscle	0.00 RPM	13.15 RPM
SRP012922_spleen	0.00 RPM	34.80 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_1591 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
Cavia porcellus	ENSCPOG00000024811	1 retrocopy	retro_cpor_1163,
Dasypus novemcinctus	ENSDNOG00000005703	2 retrocopies	retro_dnov_1591 , retro_dnov_2683,
Mus musculus	ENSMUSG00000064326	1 retrocopy	retro_mmus_2288,
Otolemur garnettii	ENSOGAG00000016881	1 retrocopy	retro_ogar_3280,