RetrogeneDB ID: retro_dord_623

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_4210:52344..52830(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Get4
• Ensembl ID: ENSDORG00000001525
• Aliases: None
• Description: golgi to ER traffic protein 4 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1914854]

Sequence

>retro_dord_623
CAAGAATACTTTGAATCTTGATTCCAGTTGTTCTTCTGAGATGGTGAGGGTTTCACCAACATGCTGGTGAAGGACTCCAC
GGCCCATTGCTTCTGCAGCAAACAGACGTGTTCTTGGCCCAGGCAGTGCTGCAGTTTCTTTATTGGAAAAACAATAGTAG
GGCGTTGTTAGTCTTCACCATGTAAGTACAGAAGCACTGTCCATTGAGGACGGCCTCCCTTTGTCCAGCCTCTGTTCCAC
TTCATCGGGTTCCTGCTGCTTGCTGTGGATGACGGCAAGCTGAGTGTGTCCACAGTGCTGTGTGAGCAGTGCCAGCCCAA
TGTATGACACGTACCTTGCCAGAACCGGACAGGACAGCTTTCCTTCATGGTGTTGCTCAAGCTTACATCTTCCTGTGGAG
GCTTTCTCGGCAACCTGCTCAGCAGCCTCCTGAGCTCCTTGGAGCAGGAAGGGGAGGAGAGGCAGGATGGTAGCAGCCCC
ATGGAG

Alignment

ORF - retro_dord_623 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.05 %
• Parental protein coverage: 51.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QNYCESRFHFLHSTDGEGCANMLVEYSTARGFRS-EVDMFVAQAVLQFLCLKNKSSALVVFTTYTQKHP-
          Q.Y.ES.F..L...DGEG..NMLV..STA..F.S...D.F.AQAVLQFL..KN.S.AL.VFT...QKH..
Retrocopy QEYFES*FQ-LFF*DGEGFTNMLVKDSTAHCFCS<QTDVFLAQAVLQFLYWKNNSRALLVFTM*VQKHC<

Parental  SIEDG-SPFVQPLL-FIWLLLLA-DGGKLTVFTVLCEQYQPSLRRDPMYNEYLDRIGQLFFGVPPKQTSS
          SIEDG..PFVQPL..FI..LLLA.D.GKL.V.TVLCEQ.QP.....P..N....R.GQL.F.V..K.TSS
Retrocopy SIEDG<PPFVQPLFHFIGFLLLAVDDGKLSVSTVLCEQCQPNV*HVPCQN----RTGQLSFMVLLKLTSS

Parental  YGGLLGNLLSSLMGSSEQEEGEESQDDSSPIE
          .GG.LGNLLSSL..S.EQ.EGEE.QD.SSP.E
Retrocopy CGGFLGNLLSSLLSSLEQ-EGEERQDGSSPME

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_623 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000001525	1 retrocopy	retro_dord_623 ,