RetrogeneDB ID: retro_dord_308

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_109767:1869..2218(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000016729
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gabarap
• Ensembl ID: ENSDORG00000005229
• Aliases: None
• Description: gamma-aminobutyric acid receptor associated protein [Source:MGI Symbol;Acc:MGI:1861742]

Sequence

>retro_dord_308
ATGAAGTTCGTGTACAAAGAAGAGCATCCGTTTGAGAAGCGCCGCTCTGAGGGCGAGAACATCAAGAAGAAATACCCGGA
CCGGTCCCGGTGATAGTAGAAAAGGCTCCTAAAGCTCGGATAGGAGATATGGACAAAAAGAAATACCTGGTGCCTTCTGA
TCTCACAGTTGGTCAATTCTATTTCTTGACCAGAAAGCGAATTCATCTCCACGCTGAGGATGCCTTGTTTTTCTTTGTCA
CAATGTCATTCCACCCACTAGTGCCACGATGGGTCAGCTCTACCAAGAACACCATAAAGAAAACTTCTTTCTATACATTG
CCTACAGTGATGAAAGTGTCTACGGTCTG

Alignment

ORF - retro_dord_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKFVYKEEHPFEKRRSEGEKIRKKYPDR-VPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIH
          MKFVYKEEHPFEKRRSEGE.I.KKYPDR.VPVIVEKAPKARIGD.DKKKYLVPSDLTVGQFYFL.RKRIH
Retrocopy MKFVYKEEHPFEKRRSEGENIKKKYPDR<VPVIVEKAPKARIGDMDKKKYLVPSDLTVGQFYFLTRKRIH

Parental  LRAEDALFFFV-NNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL
          L.AEDALFFFV..NVIPPTSATMGQLYQEHH.E.FFLYIAYSDESVYGL
Retrocopy LHAEDALFFFV<HNVIPPTSATMGQLYQEHHKENFFLYIAYSDESVYGL

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_308 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014883	1 retrocopy	retro_btau_905,
Ciona intestinalis	ENSCING00000012473	1 retrocopy	retro_cint_25,
Dipodomys ordii	ENSDORG00000005229	1 retrocopy	retro_dord_308 ,
Dipodomys ordii	ENSDORG00000013862	1 retrocopy	retro_dord_376,
Loxodonta africana	ENSLAFG00000000744	1 retrocopy	retro_lafr_61,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163,
Drosophila melanogaster	FBgn0052672	1 retrocopy	retro_dmel_23,