RetrogeneDB ID: retro_dord_398

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_16219:21209..21647(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ist1
• Ensembl ID: ENSDORG00000002409
• Aliases: None
• Description: increased sodium tolerance 1 homolog (yeast) [Source:MGI Symbol;Acc:MGI:1919205]

Sequence

>retro_dord_398
GAGAAGAAAAAAACGGAATTGGCCCAGAAGGCAAGGGTGGAGATTGCTGACTATCTAGCCACTGGGGAAGAACCAGCAAG
CTCGAATCCATGTGGAGCACATTATCCGGGACGACTACATGGTGAAGGCCATGGAGATCCTGGAGCTGTACTTTGATCTG
CTAGTGCCTCGGTATGACCTCGTCCAGTCCATAAAAGAGCTAGATCTTAGTCTATATAAATCTGAGTGTACACTGGTTGG
ACTGCTCTTCAGCTTCAGTCAGAAATGGCTGAGGTGAAAGTAATTGCTGATCTGCTCTGTGCCAAGTATAGCAAAGAATA
TGGCAAGTTATGTAGGACCAACCAGATCAGAACCGTGAATGACAGGCTAATGCACAAACTGAGTGTGGAAGCCCCACTGA
AAATCTTGGTGGAGAGATACCTGATTGAAATTGCCAAG

Alignment

ORF - retro_dord_398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.03 %
• Parental protein coverage: 52.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKKKTELAQKARKEIADYLAAG-KDERARIRVEHIIREDYLVEAMEILELYCDLLLARFGLIQSMKELDP
          EKKKTELAQKAR.EIADYLA.G.K...ARI.VEHIIR.DY.V.AMEILELY.DLL..R..L.QS.KELD.
Retrocopy EKKKTELAQKARVEIADYLATG>KNQQARIHVEHIIRDDYMVKAMEILELYFDLLVPRYDLVQSIKELDL

Parental  GLYESVSTLI-WAAPRLQSEVAELKIVADQLCAKYSKEYGKLCRTNQIGTVNDRLMHKLSVEASLKILVE
          .LY.S..TL..W.A..LQSE.AE.K..AD.LCAKYSKEYGKLCRTNQI.TVNDRLMHKLSVEA.LKILVE
Retrocopy SLYKSECTLV<WTALQLQSEMAEVKVIADLLCAKYSKEYGKLCRTNQIRTVNDRLMHKLSVEAPLKILVE

Parental  RYLIEIAK
          RYLIEIAK
Retrocopy RYLIEIAK

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_398 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015051	1 retrocopy	retro_cjac_1906,
Dipodomys ordii	ENSDORG00000002409	1 retrocopy	retro_dord_398 ,
Gorilla gorilla	ENSGGOG00000001863	1 retrocopy	retro_ggor_1446,
Mustela putorius furo	ENSMPUG00000007857	1 retrocopy	retro_mputfur_415,
Pongo abelii	ENSPPYG00000007522	1 retrocopy	retro_pabe_1695,
Sus scrofa	ENSSSCG00000002743	1 retrocopy	retro_sscr_349,