RetrogeneDB ID: retro_dord_574

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_35010:9218..9708(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000010351
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Polr2g
• Ensembl ID: ENSDORG00000015696
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide G [Source:MGI Symbol;Acc:MGI:1914960]

Sequence

>retro_dord_574
ATCTCCCTGGAGCACGAGATCCTGCTGCATCCGCGGTACTTCGACCCTAACTTGCTCAACACGGTGAAGCAAAAGCTATT
CACGGAGGTGGAGGGGACGTGCACCGGGAAATACGGCTTTGTAATTGCTGTCACCACCATCGACAATATGGGTGCAGGTG
TGATCCAACCTGGGCGAGGCTTTGTCCTTTATCCAGTTAAGTACAAAGCCATTGTTTTCCAGCCCTTTAAAGGTGAAGTT
GTGGATGCTGTGGTCACTCAGGTGAACAAGGTTGGACTTTTCACTGAAATTGGGCCCATGTCTTCCTTTATCTCCCATCA
TTCCATCCCATCAGAGATGGAGTTTGATCCAAACTCCAACCCACCTTGTTACAAGACAACGGATGAGACATTGTGATTCA
GCGGGATGACGAGATCCGCTTGAAATTGTAGGGACCCGCGTGACAGATGACATTTTTGCTATTGACTCCCTGATGGATGA
TTATTTGGGG

Alignment

ORF - retro_dord_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.81 %
• Parental protein coverage: 98.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKA
          ISLEHEILLHPRYF.PNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDN.GAGVIQPGRGFVLYPVKYKA
Retrocopy ISLEHEILLHPRYFDPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNMGAGVIQPGRGFVLYPVKYKA

Parental  IVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTTDE-DIVIQQDDEI
          IVF.PFKGEVVDAVVTQVNKVGLFTEIGPMS.FIS.HSIPSEMEFDPNSNPPCYKTTDE.DIVIQ.DDEI
Retrocopy IVFQPFKGEVVDAVVTQVNKVGLFTEIGPMSSFISHHSIPSEMEFDPNSNPPCYKTTDE<DIVIQRDDEI

Parental  RLK-IVGTRVDKNDIFAIGSLMDDYLG
          RLK.IVGTRV...DIFAI.SLMDDYLG
Retrocopy RLK<IVGTRV-TDDIFAIDSLMDDYLG

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_574 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018688	1 retrocopy	retro_cjac_641,
Dipodomys ordii	ENSDORG00000015696	1 retrocopy	retro_dord_574 ,
Macropus eugenii	ENSMEUG00000011547	1 retrocopy	retro_meug_139,
Myotis lucifugus	ENSMLUG00000011039	1 retrocopy	retro_mluc_261,
Pteropus vampyrus	ENSPVAG00000003481	1 retrocopy	retro_pvam_91,