RetrogeneDB ID: retro_dord_428

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_179241:1..482(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rab5c
• Ensembl ID: ENSDORG00000006819
• Aliases: None
• Description: RAB5C, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:105306]

Sequence

>retro_dord_428
GCTTTTCTAACCCAAACTGTGTGTCTTGAAGACACAACAGTAAATGTTTGAAATATGGGATACAGCTGGTCAAGAGAGAT
ACCATAGCCTAGCACCAATGTACTACAGAGGAGCACAAGCAGCCATAGTTGTGTATGATATCACAAATGAGGAGTCTTTT
GCAAGAGCGAAAAACCGGGTTAAAGAACTTCAGAGGCAAGCAAGTCCTAACATTGTAATAGCCTTATCAGGAAACAAGAC
TGATCTAGCAAACAAAAGAGCTGTAGATTTCAAGGAAGCACAGTCTTATGCAGATGACAACAGTTTGTTATTCATGGAGA
CATCAGCTAAAACATCAATGAATGTAAATGAAATATTCATGGCAATAGCTAAAAAGCTACCAAAGAATGAACCACAGAAT
CCAGGAGCAAATTCTGCTAGAGGAAGAGGAGTGGACCTTACTGAACCCACACAGAAAACCAGGAGTCAGTGTTGTAGTAA
C

Alignment

ORF - retro_dord_428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.85 %
• Parental protein coverage: 74.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AFLTQTVCLDDTTVK-FEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASP
          AFLTQTVCL.DTTV..FEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITN...FARAKN.VKELQRQASP
Retrocopy AFLTQTVCLEDTTVN>FEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNRVKELQRQASP

Parental  NIVIALAGNKADLANKRAVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKLPKNEPQNAAGAPG
          NIVIAL.GNK.DLANKRAV.F.EAQ.YADDNSLLFMETSAKT.MNVNEIFMAIAKKLPKNEPQN......
Retrocopy NIVIALSGNKTDLANKRAVDFKEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKNEPQNPGANSA

Parental  RNRGVDLQENNPASRSQCCSN
          R.RGVDL.E.....RSQCCSN
Retrocopy RGRGVDLTEPTQKTRSQCCSN

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_428 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Dipodomys ordii	ENSDORG00000004732	1 retrocopy	retro_dord_457,
Dipodomys ordii	ENSDORG00000006819	1 retrocopy	retro_dord_428 ,
Dipodomys ordii	ENSDORG00000012429	1 retrocopy	retro_dord_288,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,
Rattus norvegicus	ENSRNOG00000018568	2 retrocopies	retro_rnor_393, retro_rnor_73,