RetrogeneDB ID: retro_dord_484

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_22560:11786..12044(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif1ax
• Ensembl ID: ENSDORG00000011536
• Aliases: None
• Description: eukaryotic translation initiation factor 1A, X-linked [Source:MGI Symbol;Acc:MGI:1913485]

Sequence

>retro_dord_484
TATGCTCAGGTGCTCAAAATGTTGGGAAATGGATGATTAGAAGCAATGTGTTTTGATGGTGTAAAGAGGTTATGTCATAT
TAGAGGGAAATTGAGAAAAAAAGTTTGGATAAATACCTCAGACATCATATTGGTTGATTTCTGTGACTATCAGGATCACA
AAGTCGATGCAATTTTAAAATACAATGCAGATGAAGCAAGAAGTCTGAAGGCATATGGCGAGCCTCCAGAAAATGCTAAA
ATCAATGAAACTGATTCA

Alignment

ORF - retro_dord_484 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.21 %
• Parental protein coverage: 59.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEARSLK
          YAQV.KMLGNG.LEAMCFDGVKRLCHIRGKLRKKVWINTSDIILV...DYQD.K.D.ILKYNADEARSLK
Retrocopy YAQVLKMLGNG*LEAMCFDGVKRLCHIRGKLRKKVWINTSDIILVDFCDYQDHKVDAILKYNADEARSLK

Parental  AYGELPEHAKINETDT
          AYGE.PE.AKINETD.
Retrocopy AYGEPPENAKINETDS

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_484 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Dipodomys ordii	ENSDORG00000011536	1 retrocopy	retro_dord_484 ,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Gorilla gorilla	ENSGGOG00000012186	3 retrocopies	retro_ggor_1103, retro_ggor_363, retro_ggor_968,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Pteropus vampyrus	ENSPVAG00000003521	2 retrocopies	retro_pvam_780, retro_pvam_92,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,