RetrogeneDB ID: retro_dord_305

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_108840:556..872(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rab1
• Ensembl ID: ENSDORG00000002112
• Aliases: None
• Description: RAB1, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:97842]

Sequence

>retro_dord_305
CTTCTTAGGTTTGCAGATGATACACACACAGAAAGCTACACCAGCACAACTGATGTGGGTCTTAGAATAAGAACTATAGA
GTTAGATGGGAAAACAATCACGCTTCAAATGTGAGAGGAATACATAGCAGGCCAAGAAAGATTTTGAACAACCATCTCCA
GCAATTGCAAAGGAAACTGTGGTAGCCTAGTTGTGCCGGATATGAATGTATAGGAGTCCTTTCAATAATGTTAAACAGCA
ACTATAGGAAATAGGTCCTTATGCCAGTGAAAATATCAACAACTTGTGAATAGGGAACCAATGTGCTCTGACCACC

Alignment

ORF - retro_dord_305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.26 %
• Parental protein coverage: 52.28 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWD--TAGQERFRTITSSYYRGAHGIIVVYDVTD
          LLRFADDT.TESY.ST..V...IRTIELDGKTI.LQ......AGQERF.T..SS...G..G..VV.D...
Retrocopy LLRFADDTHTESYTSTTDVGLRIRTIELDGKTITLQM*EEYIAGQERF*TTISSNCKGNCGSLVVPDMNV

Parental  QES-FNNVKQWLQEIDRYASENVNKLLVGNKCDLTT
          .ES.FNNVKQ.L.EI..YASEN.N.L..GN.C.LTT
Retrocopy *ES>FNNVKQQL*EIGPYASENINNL*IGNQCALTT

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_305 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000002112	1 retrocopy	retro_dord_305 ,
Macaca mulatta	ENSMMUG00000021721	1 retrocopy	retro_mmul_951,
Rattus norvegicus	ENSRNOG00000004992	1 retrocopy	retro_rnor_110,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,