RetrogeneDB ID: retro_dord_762

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_81286:3440..3679(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Isca2
• Ensembl ID: ENSDORG00000014857
• Aliases: None
• Description: iron-sulfur cluster assembly 2 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1921566]

Sequence

>retro_dord_762
TCAGGGCTAAGGGCTGTAGCTCTCCAAGTGGTCATTCCCTGCGGAGGAGCAGATTCCTCCTGATCTTTCCTGGACTTCAG
AGGCACTGGGATGCGTCGCCCTCCAACTCTGAGGCCAGCGAAGCGCAAACCCACTTCATGGACAGCTGTGTCAGGAGGCT
TCTGGAAATCACAGAAGGGTCAGAATTCCTAAGGCTGCAGGTGGAGGGAGGTGCATGCTCCGGATTCCAATCCAGTTAT

Alignment

ORF - retro_dord_762 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.6 %
• Parental protein coverage: 51.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPIAAAALRAAIPW-RRSRILLISPGLQRRWDASSSNSEAGEEQIRLTDSCVRRLLEITEGSEFLRLQVE
          S...A.AL...IP..RRSR.LLI.PGLQR.WDAS.SNSEA.E.Q....DSCVRRLLEITEGSEFLRLQVE
Retrocopy SGLRAVALQVVIPC<RRSRFLLIFPGLQRHWDASPSNSEASEAQTHFMDSCVRRLLEITEGSEFLRLQVE

Parental  GGGCSGFQYKF
          GG.CSGFQ...
Retrocopy GGACSGFQSSY

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_762 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020479	1 retrocopy	retro_cjac_1450,
Dipodomys ordii	ENSDORG00000014857	1 retrocopy	retro_dord_762 ,
Gorilla gorilla	ENSGGOG00000012894	1 retrocopy	retro_ggor_1610,
Macaca mulatta	ENSMMUG00000006566	1 retrocopy	retro_mmul_643,
Nomascus leucogenys	ENSNLEG00000016268	1 retrocopy	retro_nleu_2754,
Ochotona princeps	ENSOPRG00000011684	2 retrocopies	retro_opri_1068, retro_opri_124,
Pan troglodytes	ENSPTRG00000006536	1 retrocopy	retro_ptro_1504,
Rattus norvegicus	ENSRNOG00000012085	1 retrocopy	retro_rnor_1009,