RetrogeneDB ID: retro_dord_369

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_14397:27599..28067(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2f6
• Ensembl ID: ENSDORG00000013213
• Aliases: None
• Description: E2F transcription factor 6 [Source:MGI Symbol;Acc:MGI:1354159]

Sequence

>retro_dord_369
GGGTCTGACCTTAACAACTTTGGAGCAGTGCCCCAACCAAAGAAGCTGCAGGAGGAGATTTCCAACCTGTCCGACATGGA
AGATGCTTTGGATGAGTTAACCAAGGGCTGTGCTCAGCAGTTGTTTGAGTTAACTGACGACAAGGAAAATGAGGGGCTGG
CCTAGGTCACCTATCAGGACATTCACAACATCCAGGCCCTCCAGGAGCAGATTGTCATCACAGTGAAGGCGCCTGAGGAG
ACCAGGTTAGATGTGCCAGCTCCCAGAGAAGACTAAATCACGGTGCACATCCGAAGCACCAAGGGGCCCATTGACGTGTA
CCTCTGTGAGGTGGAGCAGACCCACCTGAAGAGCAAGACCTCCGATGGAGCCGAGGCCTCCTCCTCTAAGATCAAACATC
CAAAAGGTTCTGGGAAAGAAGAAAATCCTCAGTAAAGTAAAAAAGAGTCGCCTGAAGTGAGCAGTGGA

Alignment

ORF - retro_dord_369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSDLNNFGAVPQQKKLQEELSNLSAMEDALDELIKDCAQQLFELTDDKENERLAYVTYQDIHNIQAFHEQ
          GSDLNNFGAVPQ.KKLQEE.SNLS.MEDALDEL.K.CAQQLFELTDDKENE.LA.VTYQDIHNIQA..EQ
Retrocopy GSDLNNFGAVPQPKKLQEEISNLSDMEDALDELTKGCAQQLFELTDDKENEGLA*VTYQDIHNIQALQEQ

Parental  IVIAVKAPEETRLDVPAPREDSITVHIRSTKGPIDVYLCEVEQTHPKGKTSDGASASSSKSKHPKGSGKE
          IVI.VKAPEETRLDVPAPRED.ITVHIRSTKGPIDVYLCEVEQTH.K.KTSDGA.ASSSK.KHPKGSGKE
Retrocopy IVITVKAPEETRLDVPAPRED*ITVHIRSTKGPIDVYLCEVEQTHLKSKTSDGAEASSSKIKHPKGSGKE

Parental  ENPQ---EESPEVSSG
          ENPQ....ESPEVSSG
Retrocopy ENPQ*SKKESPEVSSG

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_369 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 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005114	5 retrocopies	retro_chof_1613, retro_chof_2316, retro_chof_2487, retro_chof_2627, retro_chof_537,
Dipodomys ordii	ENSDORG00000013213	1 retrocopy	retro_dord_369 ,
Macropus eugenii	ENSMEUG00000007957	4 retrocopies	retro_meug_1169, retro_meug_860, retro_meug_882, retro_meug_893,
Myotis lucifugus	ENSMLUG00000003384	1 retrocopy	retro_mluc_864,
Otolemur garnettii	ENSOGAG00000013601	2 retrocopies	retro_ogar_2337, retro_ogar_3080,