RetrogeneDB ID: retro_dord_86

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_2551:219506..220164(+)
• Located in intron of: ENSDORG00000007320

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nup54
• Ensembl ID: ENSDORG00000001341
• Aliases: None
• Description: nucleoporin 54 [Source:MGI Symbol;Acc:MGI:1920460]

Sequence

>retro_dord_86
GGTGGTCTCTTCAGTCAGCCTACACAAGCTTCTACCTAGTCCAACCAACTGATAAATACTCCAAGTGCTCTTTCTCCTCT
AACATTATTGGGAGATGAGAGAGATGCTATTTTGGCAAAATAGAATCAACTGCAAAGCCTTCTGGGGAACAGGAAAAGGA
TATTTCAACAATAATACTCCTCCAGTTGAATTTACATAAGAAAATCCCTTTTGTCGATTTAAAGCTGTAGTTATAGCTGT
ATGCCAAATAATAAAGATGAAGATGGTCTATTGGGTTTTAGTTTTCACAAAAAAGAAACAGATATTCGAAATTAACAACA
GCAGTTGATAGAATCATTACATAAAGTTTTGGGAGGAAACCAGACCTTACTGTAAATGTAGAGGGTATTAAAACATTGTC
AGATGATCAGACAGAAGTTGTCATTTATGTTGTTGAGCATTCTCTAATGGTACCTCAAGAAGAGTTCCAGCTACAATACT
CTATTCCCATTTTGAACAAGCCAATATAAAAACACAGTTGCAGCAACTTGGTGTCACACTTTCTATAGCAAAAACAGAAC
TTTCTCCTGTACAGATCAAACAGCTTTTACAGAATCCTCCTGCTGGTGTTGATCCTATTATTTGGGAACAAGCCAAGGAG
GATAACCTTGATTCTGAA

Alignment

ORF - retro_dord_86 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.05 %
• Parental protein coverage: 53.92 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GGLFSQPTQAPTQSNQLINTASALSAPTLLGDERDAILAKWNQLQ-AFWGTGKGYFNNNIPPVEFTQENP
          GGLFSQPTQA.T.SNQLINT.SALS..TLLGDERDAILAK.NQLQ.AFWGTGKGYFNNN.PPVEFT.ENP
Retrocopy GGLFSQPTQAST*SNQLINTPSALSPLTLLGDERDAILAK*NQLQ>AFWGTGKGYFNNNTPPVEFT*ENP

Parental  FCRFKAV-GYSCMPNNKDEDGLVVLVFNKKETDIRNQQQQLVESLHKVLGGNQTL-TVNVEGIKTLPDDQ
          FCRFKAV..YSCMPNNKDEDGL....F.KKETDIRN.QQQL.ESLHKVLGGNQTL.TVNVEGIKTL.DDQ
Retrocopy FCRFKAV<SYSCMPNNKDEDGLLGFSFHKKETDIRN*QQQLIESLHKVLGGNQTL<TVNVEGIKTLSDDQ

Parental  TEVVIYVVERS-PNGTSRRVPATILYSHFEQANIKTQLQQLGVTLSMTRTELSPAQIKQLLQNPPAGVDP
          TEVVIYVVE.S..NGTSRRVPATILYSHFEQANIKTQLQQLGVTLS...TELSP.QIKQLLQNPPAGVDP
Retrocopy TEVVIYVVEHS<SNGTSRRVPATILYSHFEQANIKTQLQQLGVTLSIAKTELSPVQIKQLLQNPPAGVDP

Parental  IIWEQAKVDNRDSE
          IIWEQAK.DN.DSE
Retrocopy IIWEQAKEDNLDSE

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_86 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
Dipodomys ordii	ENSDORG00000001341	1 retrocopy	retro_dord_86 ,
Myotis lucifugus	ENSMLUG00000005318	1 retrocopy	retro_mluc_1042,
Mus musculus	ENSMUSG00000034826	1 retrocopy	retro_mmus_484,