RetrogeneDB ID: retro_dord_24

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_3843:20370..20982(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000015066
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000010504
• Aliases: None
• Description: None

Sequence

>retro_dord_24
ATGAGTATGGAAGATTATGACTTCCTGTTCAAAATCGTTTTAATTGGCAACGCCGGTGTGGGGAAGACGTGCCTAGTCCG
ACGATTCACTCAGGGTCTTTTCCCCCCAGGTCAAGGAGCCACAATTGGAGTTGATTTTATGATTAAGACAGTGGAGATCA
ATGGTGAAAAAGTAAAGCTACAGATCTGGGACACTGCAGGACAGGAGAGATTTCACTCCATTACCCAGAGTTATTACCGC
AGCGCCAATGCCTTGATCCTTACCTATGACATTACCTGTGAGGAATCCTTCCACTGCCTTCCTGAGTGGCTGCGAGAGAT
AGAACAGTATGCCAGCAACAAGGTCATCACCGTGCTAGTGGGCAACAAGATTGACCTGGCTGACAGGAGAGAGGTCTCCC
AGCAGAGAGCTGAGGAATTCTCAGAAGCTCAGGACATGTGTTACCTGGAGACTTCAGCCAAGGAATCAGATAACGTAGAG
AAACTCTTCCTTGACTTAGCATGCCGACTCATCAGAGAAGCCAGACAGAACACACTGGTGAACAATGTATCCTCCCCCTT
ACCCAGAGAAGGGAAAAGCATCAGCTATTTGACTTGCTGTAATTTCAACTAA

Alignment

ORF - retro_dord_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSMEDYDFLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEINGEKVKLQIWDTAGQER
          MSMEDYDFLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEINGEKVKLQIWDTAGQER
Retrocopy MSMEDYDFLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEINGEKVKLQIWDTAGQER

Parental  FRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYASNKVITVLVGNKIDLADRREVSQQRAEEF
          F.SITQSYYRSANALILTYDITCEESF.CLPEWLREIEQYASNKVITVLVGNKIDLADRREVSQQRAEEF
Retrocopy FHSITQSYYRSANALILTYDITCEESFHCLPEWLREIEQYASNKVITVLVGNKIDLADRREVSQQRAEEF

Parental  SEAQDMYYLETSAKESDNVEKLFLDLACRLIREARQNTLVNNVSSPLPGEGKSISYLTCCNFN
          SEAQDM.YLETSAKESDNVEKLFLDLACRLIREARQNTLVNNVSSPLP.EGKSISYLTCCNFN
Retrocopy SEAQDMCYLETSAKESDNVEKLFLDLACRLIREARQNTLVNNVSSPLPREGKSISYLTCCNFN

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_24 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	ENSDORG00000010504	1 retrocopy	retro_dord_24 ,