RetrogeneDB ID: retro_dord_519

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_25872:6774..7047(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Apitd1
• Ensembl ID: ENSDORG00000006387
• Aliases: None
• Description: apoptosis-inducing, TAF9-like domain 1 [Source:MGI Symbol;Acc:MGI:1917178]

Sequence

>retro_dord_519
GAGGAGGGAGAGGAAGCCAAGGAGCAACAGTGATTCTCTTACCAGCACAGGCTAAAGGCTGTAGTTCACTATACAGTTGG
TTGCCTTTGCAAAGAAGTTGAATTGGACAAAGAGATGCCGTTTGGCAAACAGACCATTGCAACAATCTTGGATCTGACTT
TTCAGCAATGCAATAATTTTGCCAAAGACCTTGAGATGTTTGTCAGACACGCGAAAAGAAGCACAATTAACACTGATGAC
ATGAATCTCTTAGTGAGAAGAACCAGAAGATTG

Alignment

ORF - retro_dord_519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.32 %
• Parental protein coverage: 54.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEGEEAEEQQRFSYQQRLKAAVHYTVGCLCKEVELDKEMPFSKQTIAAISELTFRQCDNFAKDLEMFARH
          EEGEEA.EQQ.FSYQ.RLKA.VHYTVGCLCKEVELDKEMPF.KQTIA.I..LTF.QC.NFAKDLEMF.RH
Retrocopy EEGEEAKEQQ*FSYQHRLKAVVHYTVGCLCKEVELDKEMPFGKQTIATILDLTFQQCNNFAKDLEMFVRH

Parental  AKRSTINTDDVKLLARRSNSL
          AKRSTINTDD..LL.RR...L
Retrocopy AKRSTINTDDMNLLVRRTRRL

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_519 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004967	1 retrocopy	retro_chof_1934,
Dipodomys ordii	ENSDORG00000006387	1 retrocopy	retro_dord_519 ,
Macropus eugenii	ENSMEUG00000004963	1 retrocopy	retro_meug_878,