RetrogeneDB ID: retro_dord_457

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_19949:14225..14705(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rab21
• Ensembl ID: ENSDORG00000004732
• Aliases: None
• Description: RAB21, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:894308]

Sequence

>retro_dord_457
GCGGCCAGTGGTTTGGTGGCTGAGGCGGGCCGAGCCTCCTCCTTCAAGGTGGTGCTGCTCCGAGAAGGCTGCTTGGGGAA
GACGTCGCTGGTGCTGCGCTGTTGCGAGAACAAGTTCAAGGACAAGCACATCACCACTCTGCAGGCGTCTTTCTTAACAA
CGAAGTTACATATCGGTGGGAAAAGAGTTAATCTTGCTATATGGGATACAGTGGGTCAAGAGAGATTCCATGCATTAGGT
CCTCTTTACTACAGAGATTCAAATGGAGCTATTTTAGTTTATTATAGAGCAGATGAAGATTCTTTTCAGAAGGTAAAAAA
CTGGGTCAAAGAATTACAGAAAATGTTGGGAAATGAAATCTGTTTATGTATAGTGGGTAATAAAATAGATTTGGAAAAAG
AGAGACATGTGTCCATTCAAGAAGCGGAATCATGTGCAGAGTCTGTGGGAGAAAAACATTATCCTACTTCAGCCAAACAA

Alignment

ORF - retro_dord_457 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 72.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAGGGAAAGRAYSFKVVLLGEGCVGKTSLVLRYCENKFNDKHITTLQASFLTKKLNIGGKRVNLAIWDT
          AA.G..A.AGRA.SFKVVLL.EGC.GKTSLVLR.CENKF.DKHITTLQASFLT.KL.IGGKRVNLAIWDT
Retrocopy AASGLVAEAGRASSFKVVLLREGCLGKTSLVLRCCENKFKDKHITTLQASFLTTKLHIGGKRVNLAIWDT

Parental  AGQERFHALGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEKERHVSIQ
          .GQERFHALGP.YYRDSNGAILVY...DEDSFQKVKNWVKEL.KMLGNEICLCIVGNKIDLEKERHVSIQ
Retrocopy VGQERFHALGPLYYRDSNGAILVYYRADEDSFQKVKNWVKELQKMLGNEICLCIVGNKIDLEKERHVSIQ

Parental  EAESYAESVGAKHYHTSAKQ
          EAES.AESVG.KHY.TSAKQ
Retrocopy EAESCAESVGEKHYPTSAKQ

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_457 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000004732	1 retrocopy	retro_dord_457 ,
Dipodomys ordii	ENSDORG00000006819	1 retrocopy	retro_dord_428,
Dipodomys ordii	ENSDORG00000012429	1 retrocopy	retro_dord_288,
Microcebus murinus	ENSMICG00000009168	1 retrocopy	retro_mmur_176,
Myotis lucifugus	ENSMLUG00000013239	1 retrocopy	retro_mluc_2070,
Ochotona princeps	ENSOPRG00000011037	1 retrocopy	retro_opri_378,