RetrogeneDB ID: retro_dord_581

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_35446:4325..4592(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Emc4
• Ensembl ID: ENSDORG00000008407
• Aliases: None
• Description: ER membrane protein complex subunit 4 [Source:MGI Symbol;Acc:MGI:1915282]

Sequence

>retro_dord_581
ACACGGCCCATCTTCCCTACCATGATGGTGTGCGTGATGGCCTGGCAGCCGGTCCAAGCCGTCATGGCCATTTCAGCCAT
TTTCAAGATGTTAGAGAGTTCAAGCCAGAAGTTTCTTCAGGGTCTGGTTTATCTCATTGGGAACCTCATGGGCTTGGCAC
TGGCTGTTTAGAAGTCCATGGGTCTGTTACCTACGCATGCATCAGATTGGTTAGCCTTCATCAAACCTCTGGAGAGCATG
GAGTCCAGTGGTGGAGGACTCGTTTTG

Alignment

ORF - retro_dord_581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 78.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TISIFPTMMVCMMAWRPVQALMAI-ATFKMLESSSQKFLQGLVYLIGNLMGLALAVYKCQSMGLLPTHAS
          T..IFPTMMVC.MAW.PVQA.MAI.A.FKMLESSSQKFLQGLVYLIGNLMGLALAV.K..SMGLLPTHAS
Retrocopy TRPIFPTMMVCVMAWQPVQAVMAISAIFKMLESSSQKFLQGLVYLIGNLMGLALAV*K--SMGLLPTHAS

Parental  DWLAFIEPPERMEFSGGGLVL
          DWLAFI.P.E.ME.SGGGLVL
Retrocopy DWLAFIKPLESMESSGGGLVL

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_581 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005576	2 retrocopies	retro_chof_1859, retro_chof_254,
Dipodomys ordii	ENSDORG00000008407	2 retrocopies	retro_dord_387, retro_dord_581 ,
Echinops telfairi	ENSETEG00000001688	1 retrocopy	retro_etel_1631,
Felis catus	ENSFCAG00000001736	1 retrocopy	retro_fcat_759,
Macropus eugenii	ENSMEUG00000004615	1 retrocopy	retro_meug_1129,
Microcebus murinus	ENSMICG00000003864	2 retrocopies	retro_mmur_1313, retro_mmur_180,
Oryctolagus cuniculus	ENSOCUG00000006160	4 retrocopies	retro_ocun_1686, retro_ocun_395, retro_ocun_719, retro_ocun_817,
Ochotona princeps	ENSOPRG00000009190	1 retrocopy	retro_opri_605,
Pteropus vampyrus	ENSPVAG00000003824	1 retrocopy	retro_pvam_386,
Rattus norvegicus	ENSRNOG00000005719	1 retrocopy	retro_rnor_897,
Ictidomys tridecemlineatus	ENSSTOG00000000516	1 retrocopy	retro_itri_1008,