RetrogeneDB ID: retro_dord_523

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_2655:87675..88110(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Agpat5
• Ensembl ID: ENSDORG00000008708
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon) [Source:MGI Symbol;Acc:MGI:1196345]

Sequence

>retro_dord_523
TTTTTCCCAGGAAAAGCAAAACTCCTAACTGCTAGTCAGTCATTTGCTGCCTGACAGGGCCTTCTGGTGTTCAAACATGT
GCTGACTCCAAGATTAAAGGCAACTCGCGTTGCTTTGGTCTCTCTGAAGAGTTACCTCAATGCCATTGACGACGTTACAG
TGGTTTACAAAGGGAAGAGTGCGAAGTCGTAGCAGCCGGAGGAGCCTCTGTACCTATCAGGTTTTCTATGCAAAGAATGT
CCAAAAAATTCACATTGATCGTATCAGCAGAAAAGATGTTCCAGAAAGACAAACATCTCTGAGAAGATGGCTTCACCAAC
GTGTTGAGATCAAAGACAAGTTCTTATAGAATTTTCTGATTGACCAGATCCAGCAAGAAGAAACAAATTTCCTGGGAAAA
GTGTTCATTTCATAGTAAGTGTCAAGAAGATCTTA

Alignment

ORF - retro_dord_523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.89 %
• Parental protein coverage: 50.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FSPGQTKLLSASQAFAAEHGLPVLKHVLTPRVKATYVAFDSLKSYLDAIYDITVVYEGRSANWQQRQQQE
          F.PG..KLL.ASQ.FAA..GL.V.KHVLTPR.KAT.VA..SLKSYL.AI.D.TVVY.G.SA.....Q..E
Retrocopy FFPGKAKLLTASQSFAA*QGLLVFKHVLTPRLKATRVALVSLKSYLNAIDDVTVVYKGKSA--KS*QPEE

Parental  PLTMTEFLCKEC-VKIHIHIDRIDKKDVPEEQAYMRRWLHERFEIKDK-LLIEFFDSPDPARRNKFPGKS
          PL....FLCKEC..KIH..IDRI..KDVPE.Q...RRWLH.R.EIKDK..LIEF.D.PDPARRNKFPGKS
Retrocopy PLYLSGFLCKEC>QKIH--IDRISRKDVPERQTSLRRWLHQRVEIKDK<VLIEFSD*PDPARRNKFPGKS

Parental  VHSKLSLKKTL
          VH...S.KK.L
Retrocopy VHFIVSVKKIL

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_523 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005142	1 retrocopy	retro_chof_376,
Dasypus novemcinctus	ENSDNOG00000004979	1 retrocopy	retro_dnov_823,
Dipodomys ordii	ENSDORG00000008708	1 retrocopy	retro_dord_523 ,
Ochotona princeps	ENSOPRG00000014343	3 retrocopies	retro_opri_343, retro_opri_829, retro_opri_935,
Sarcophilus harrisii	ENSSHAG00000000051	1 retrocopy	retro_shar_687,
Tupaia belangeri	ENSTBEG00000013084	1 retrocopy	retro_tbel_2948,