RetrogeneDB ID: retro_dord_374

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_14693:5796..6275(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rexo2
• Ensembl ID: ENSDORG00000011255
• Aliases: None
• Description: REX2, RNA exonuclease 2 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1888981]

Sequence

>retro_dord_374
GGTCCCAACCCGATTATACAATAACCAAATGAACTGCTGGACAGCAGGTCCGATGGTGTAAGGAGCATCATGCGAAGTCT
GGTCTTACCAAGGCAGTGGAGGGGAGTACAATCACATTGCAGCAGGCAGAGTATGAATTTCTGTCCTTTGTACAGCAGCA
GACCCCTCCGGGGCTCTGTCGGCTTGCAGGAAATTCAGTTCATGCAGATAAGAAGTTTCTTGACAAATGTGTGCCACAGT
TCATGAAACATCTTCATTATAGAATAATTGACGTGAGCACTGTTAAAGAACTGTGCAGACGCTGGTATCCAGAAGAATAT
GCATTTGCACCAAAGAAGGCTGCTTCTCACAGGGCCCTTAATGACATTAGTGAAAGCATCAAAGAGCTTCAGTTTTACCA
AAATAATATTTTCAAGAAAAAAACAGATGAGAAGAAGAGGAAAATTATAGAAAATGAGGAGAATGAGAAGACAGTGAGT

Alignment

ORF - retro_dord_374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.44 %
• Parental protein coverage: 67.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPNLIIKQPDELLDSMSD-WCKEHHGKSGLTKAVKESTITLQQAEYEFLSFVRQQTPPGLCPLAGNSVHA
          GPN.II..P.ELLDS.SD.WCKEHH.KSGLTKAV..STITLQQAEYEFLSFV.QQTPPGLC.LAGNSVHA
Retrocopy GPNPIIQ*PNELLDSRSD<WCKEHHAKSGLTKAVEGSTITLQQAEYEFLSFVQQQTPPGLCRLAGNSVHA

Parental  DKKFLDKYMPQFMKHLHYRIIDVSTVKELCRRWYPEEYEFAPKKAASHRALDDISESIKELQFYRNNIFK
          DKKFLDK..PQFMKHLHYRIIDVSTVKELCRRWYPEEY.FAPKKAASHRAL.DISESIKELQFY.NNIFK
Retrocopy DKKFLDKCVPQFMKHLHYRIIDVSTVKELCRRWYPEEYAFAPKKAASHRALNDISESIKELQFYQNNIFK

Parental  KKTDEKKRKIIENGENEKTVS
          KKTDEKKRKIIEN.ENEKTVS
Retrocopy KKTDEKKRKIIENEENEKTVS

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_374 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013497	1 retrocopy	retro_chof_40,
Callithrix jacchus	ENSCJAG00000012434	1 retrocopy	retro_cjac_1493,
Dipodomys ordii	ENSDORG00000011255	1 retrocopy	retro_dord_374 ,
Equus caballus	ENSECAG00000005988	1 retrocopy	retro_ecab_572,
Myotis lucifugus	ENSMLUG00000009030	1 retrocopy	retro_mluc_1861,
Monodelphis domestica	ENSMODG00000013913	1 retrocopy	retro_mdom_1575,
Tarsius syrichta	ENSTSYG00000002237	1 retrocopy	retro_tsyr_1177,