RetrogeneDB ID: retro_dord_179

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_470:187221..187560(+)
• Located in intron of: ENSDORG00000001499

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif1b
• Ensembl ID: ENSDORG00000013689
• Aliases: None
• Description: eukaryotic translation initiation factor 1B [Source:MGI Symbol;Acc:MGI:1916219]

Sequence

>retro_dord_179
ATGTCCGCTATCCAGAACCTCCATTCTTTCGACCCCTTTGCTGATGCAAGTAAGGGTGATGACCTGCTTCCTGCTGGCAC
TGAGGAATATATCCATATAAGAATTCAACAGAGAAACGTTAGGAAGACCCTTACTACTGTCCAAAGGATCGCTGATGATT
ACGATAAAAAGAAACTAGTGAAGGCGTTTAAGAAGAAATTTGCCTGCAATGGTACTGTAATTGAGCATCCAGAATATGGA
GAAGTAATTCAGCTACAGGGTGACCAGCGCAAGAACATATGCCAGTTCCTGGTAGAGATTGGACTGGCTAAGGACGATCA
GCTGAAGGTTCATGGGTTT

Alignment

ORF - retro_dord_179 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTIQNLQSFDPFADATKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACN
          MS.IQNL.SFDPFADA.KGDDLLPAGTE.YIHIRIQQRN.RKTLTTVQ.IADDYDKKKLVKAFKKKFACN
Retrocopy MSAIQNLHSFDPFADASKGDDLLPAGTEEYIHIRIQQRNVRKTLTTVQRIADDYDKKKLVKAFKKKFACN

Parental  GTVIEHPEYGEVIQLQGDQRKNICQFLLEVGIVKEEQLKVHGF
          GTVIEHPEYGEVIQLQGDQRKNICQFL.E.G..K..QLKVHGF
Retrocopy GTVIEHPEYGEVIQLQGDQRKNICQFLVEIGLAKDDQLKVHGF

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_179 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 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013689	4 retrocopies	retro_dord_179 , retro_dord_307, retro_dord_626, retro_dord_669,
Dipodomys ordii	ENSDORG00000013853	4 retrocopies	retro_dord_349, retro_dord_350, retro_dord_663, retro_dord_753,
Echinops telfairi	ENSETEG00000017295	5 retrocopies	retro_etel_1228, retro_etel_1480, retro_etel_1793, retro_etel_31, retro_etel_4,
Microcebus murinus	ENSMICG00000013223	5 retrocopies	retro_mmur_254, retro_mmur_445, retro_mmur_535, retro_mmur_654, retro_mmur_706,
Macaca mulatta	ENSMMUG00000017704	1 retrocopy	retro_mmul_154,
Monodelphis domestica	ENSMODG00000011056	2 retrocopies	retro_mdom_1113, retro_mdom_1382,
Mus musculus	ENSMUSG00000006941	1 retrocopy	retro_mmus_587,
Otolemur garnettii	ENSOGAG00000025224	1 retrocopy	retro_ogar_1943,
Ictidomys tridecemlineatus	ENSSTOG00000012168	1 retrocopy	retro_itri_1597,
Tupaia belangeri	ENSTBEG00000013185	6 retrocopies	retro_tbel_1861, retro_tbel_1920, retro_tbel_1996, retro_tbel_2954, retro_tbel_3209, retro_tbel_3867,
Tarsius syrichta	ENSTSYG00000006338	3 retrocopies	retro_tsyr_1574, retro_tsyr_2154, retro_tsyr_888,