RetrogeneDB ID: retro_dord_708

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_59257:7641..7968(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000002749
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gm5334
• Ensembl ID: ENSDORG00000012580
• Aliases: None
• Description: predicted pseudogene 5334 [Source:MGI Symbol;Acc:MGI:3644545]

Sequence

>retro_dord_708
TATGCCATGTTCCTGTGCCTGATGTTTCTGGCTGAGCTTGTAGCTGGCATTTCAGGGTTTGTGTTTCGTCATGAGATCAA
GGACACCTTCCTAAGGACTTGCACGGATGCCATGCAGAACTACAATGGCAATAATGAGAGAAGCCGTACGGTGGACCATG
TGCAGCGCAGCCTAAGCTGCTGTGGCGTGCAGAACTACACCAACTGGAGCACCAGCCCCTATTTCCTGGAGCATGGCATC
CCCCCAAGTTGCTGCATGAATGAAACCGATTGCAATCCCCAGGATCTACATTATCTGACTGTGGCTGCCACCAAAGTTAA
CCAGAAG

Alignment

ORF - retro_dord_708 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.5 %
• Parental protein coverage: 55.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YAMFLSLVFLAELVAGISGFVFRHEIKDTFLRTYTDAMQNYNGNDERSRAVDHVQRSLSCCGVQNYTNWS
          YAMFL.L.FLAELVAGISGFVFRHEIKDTFLRT.TDAMQNYNGN.ERSR.VDHVQRSLSCCGVQNYTNWS
Retrocopy YAMFLCLMFLAELVAGISGFVFRHEIKDTFLRTCTDAMQNYNGNNERSRTVDHVQRSLSCCGVQNYTNWS

Parental  TSPYFLEHGIPPSCCMNETDCNPQDLHNLTVAATKVNQK
          TSPYFLEHGIPPSCCMNETDCNPQDLH.LTVAATKVNQK
Retrocopy TSPYFLEHGIPPSCCMNETDCNPQDLHYLTVAATKVNQK

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_708 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000183	1 retrocopy	retro_cpor_716,
Dipodomys ordii	ENSDORG00000012580	1 retrocopy	retro_dord_708 ,
Macropus eugenii	ENSMEUG00000002809	1 retrocopy	retro_meug_1563,
Otolemur garnettii	ENSOGAG00000008547	2 retrocopies	retro_ogar_1615, retro_ogar_3124,