RetrogeneDB ID: retro_dord_342

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_12964:37208..37508(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Glipr2
• Ensembl ID: ENSDORG00000012831
• Aliases: None
• Description: GLI pathogenesis-related 2 [Source:MGI Symbol;Acc:MGI:1917770]

Sequence

>retro_dord_342
ATGGGCAAGTCAGCTTCCAAAGAGTTTAATAATGAAGTCCTAAAGGCCCACAATGAGTACCGGCGGCAGCATGGAGTCCC
CCCACTGAAGCTCTCCAAGAAGCTCAACCGAGAGGCTCAGCAGTATTCAGAGGCCCTGGCCAGCACAAGGATCCTCAAAC
ACAGCCCAGAGTCGAGTCGTGGCCAGTGTGGGGAGAATCTAGCATGGACATCCTATGATCAGACAGGACAGGAGGTGGCT
GATAGATGGTATGGTGAAATCAAGAACTACAACTTCCAGCAGCCTGGCTTTACCTCTGGG

Alignment

ORF - retro_dord_342 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99. %
• Parental protein coverage: 99.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKSASKEFNNEVLKAHNEYRRQHGVPPLKLSKKLNREAQQYSEALASTRILKHSPESSRGQCGENLAWA
          MGKSASKEFNNEVLKAHNEYRRQHGVPPLKLSKKLNREAQQYSEALASTRILKHSPESSRGQCGENLAW.
Retrocopy MGKSASKEFNNEVLKAHNEYRRQHGVPPLKLSKKLNREAQQYSEALASTRILKHSPESSRGQCGENLAWT

Parental  SYDQTGQEVADRWYGEIKNYNFQQPGFTSG
          SYDQTGQEVADRWYGEIKNYNFQQPGFTSG
Retrocopy SYDQTGQEVADRWYGEIKNYNFQQPGFTSG

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_342 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030686	1 retrocopy	retro_cfam_428,
Dasypus novemcinctus	ENSDNOG00000008950	1 retrocopy	retro_dnov_2040,
Dipodomys ordii	ENSDORG00000012831	1 retrocopy	retro_dord_342 ,
Felis catus	ENSFCAG00000012762	2 retrocopies	retro_fcat_115, retro_fcat_1587,
Microcebus murinus	ENSMICG00000017673	1 retrocopy	retro_mmur_1525,
Myotis lucifugus	ENSMLUG00000011791	2 retrocopies	retro_mluc_1145, retro_mluc_475,
Mus musculus	ENSMUSG00000028480	1 retrocopy	retro_mmus_2458,
Rattus norvegicus	ENSRNOG00000014838	1 retrocopy	retro_rnor_2217,
Tupaia belangeri	ENSTBEG00000009276	2 retrocopies	retro_tbel_1646, retro_tbel_4682,