RetrogeneDB ID: retro_dord_448

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_194753:358..649(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lage3
• Ensembl ID: ENSDORG00000009093
• Aliases: None
• Description: L antigen family, member 3 [Source:MGI Symbol;Acc:MGI:1913442]

Sequence

>retro_dord_448
AGAGACACTACGTCCTGCGCTGAAAGGCCTGGAGTCCAACCACCCATGTTCACCCTCAGCATGCCTTTCCCGACCCCTTT
GGAAGCCGAAATTGCCCGTGGGGCCCTGGCCCCAGATGCTGAGCCCCACCAGGGAGCACTGGGGAAGGAGCTCACAGTGA
GCGCGAGCACCGTGGCCGTACACTGGACAGCTGGAGACGCTCACCTGCTCCAGGCTTCCATCACCAGCTTCCTTGGACAG
GTTGCCCTGGTCATGCAGACCATGCAGCGCGTTGGGCCCCCTGTTGCCCGG

Alignment

ORF - retro_dord_448 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.57 %
• Parental protein coverage: 66.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RDATSCAERPGVRPHMFALSVPFPTPLEAEIARGALAPDAEPHQGALGKELTVSGSTLAVHWTAGDARLL
          RD.TSCAERPGV.P.MF.LS.PFPTPLEAEIARGALAPDAEPHQGALGKELTVS.ST.AVHWTAGDA.LL
Retrocopy RDTTSCAERPGVQPPMFTLSMPFPTPLEAEIARGALAPDAEPHQGALGKELTVSASTVAVHWTAGDAHLL

Parental  RVSIISFLEQVALVMRTMQRFGPPVAR
          ..SI.SFL.QVALVM.TMQR.GPPVAR
Retrocopy QASITSFLGQVALVMQTMQRVGPPVAR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_448 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024143	1 retrocopy	retro_dnov_244,
Dipodomys ordii	ENSDORG00000009093	1 retrocopy	retro_dord_448 ,
Homo sapiens	ENSG00000196976	1 retrocopy	retro_hsap_4244,
Gorilla gorilla	ENSGGOG00000013507	1 retrocopy	retro_ggor_2845,
Macaca mulatta	ENSMMUG00000007739	1 retrocopy	retro_mmul_1145,
Mus musculus	ENSMUSG00000015289	2 retrocopies	retro_mmus_1411, retro_mmus_1665,
Nomascus leucogenys	ENSNLEG00000014285	1 retrocopy	retro_nleu_1373,
Ochotona princeps	ENSOPRG00000003778	2 retrocopies	retro_opri_196, retro_opri_549,
Pongo abelii	ENSPPYG00000020881	1 retrocopy	retro_pabe_3394,
Rattus norvegicus	ENSRNOG00000037249	1 retrocopy	retro_rnor_595,
Sus scrofa	ENSSSCG00000025528	1 retrocopy	retro_sscr_94,