RetrogeneDB ID: retro_dord_676

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_51457:6888..7224(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Paip2
• Ensembl ID: ENSDORG00000002264
• Aliases: None
• Description: polyadenylate-binding protein-interacting protein 2 [Source:MGI Symbol;Acc:MGI:1915119]

Sequence

>retro_dord_676
GATGTGATTATTAACGGTCATTCTCATGAAGATGACAATCCACTTGCAGAGTACATGTGGATGGAAAATGAAGAGGAATT
CAACAGACAAATAGAAGAAGAGTTGTGGGAAGAAGAATTTATTGAATGTTGTTTCCAAGAAATGCTGGAGGAGGAAGAAG
AACATGAGTGGTTTATTCCAGCTTGAGATCTCCCCCAAACTATGGACCAAATCCAAGACCAATTTAATGACCTTGTTATC
AGTGATGGCTCTTCTCTGGAAGATCTTGTGGTCAAGAGCAATCTGAATCCAAATGCAAAGGAGTTTGTTCCTGGGGTGAA
GTACTAAAATATTTCA

Alignment

ORF - retro_dord_676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.43 %
• Parental protein coverage: 87.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DVIINGHSHEDDNPFAEYMWMENEEEFNRQIEEELWEEEFIERCFQEMLEEEEEHEWFIPARDLPQTMDQ
          DVIINGHSHEDDNP.AEYMWMENEEEFNRQIEEELWEEEFIE.CFQEMLEEEEEHEWFIPA.DLPQTMDQ
Retrocopy DVIINGHSHEDDNPLAEYMWMENEEEFNRQIEEELWEEEFIECCFQEMLEEEEEHEWFIPA*DLPQTMDQ

Parental  IQDQFNDLVISDGSSLEDLVVKSNLNPNAKEFVPGVKY-NIS
          IQDQFNDLVISDGSSLEDLVVKSNLNPNAKEFVPGVKY.NIS
Retrocopy IQDQFNDLVISDGSSLEDLVVKSNLNPNAKEFVPGVKY*NIS

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_676 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	ENSCJAG00000006982	1 retrocopy	retro_cjac_212,
Dipodomys ordii	ENSDORG00000002264	1 retrocopy	retro_dord_676 ,
Microcebus murinus	ENSMICG00000012451	1 retrocopy	retro_mmur_1085,
Rattus norvegicus	ENSRNOG00000019934	1 retrocopy	retro_rnor_294,
Tupaia belangeri	ENSTBEG00000004105	1 retrocopy	retro_tbel_1370,