RetrogeneDB ID: retro_dord_689

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_5599:34774..35251(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Khdrbs3
• Ensembl ID: ENSDORG00000014595
• Aliases: None
• Description: KH domain containing, RNA binding, signal transduction associated 3 [Source:MGI Symbol;Acc:MGI:1313312]

Sequence

>retro_dord_689
GAAGAAGAGTTGAGGAAAAGAGGGGAAACAAGGTACTTCCACCTCAATGATGACTTCCATGTGCTCACTGAAGTGTTTGC
TCCACCAGCAGAAGCCCGTGCCCAAATGGGACATGCTTTGGAAGAAATAAAAAAGTTCCTCACCCCTGACTACAATGACA
GACCCGGCAAGCTCAGCTTCAGGAACTAACATATCTGGATGGTGGTGCAGAGAATGCAGATGCTCCAGTGGTGTGAGGGA
AGCCAACCCTACTATAAGAGGTGTAGCCAGAGGAAGAGGATTACAGCCCAGCCAGTTGGGGGTTGGTGTACCACAAGGGA
CACCAGCTCCCAGGGGAGTCCTTTCCACCCCAGGGCCAGTGAGCCAGGGAAGAGGACTTTTTACTCCCAGGGCTAGAGGA
ATGCCTCCAAGTGGGTATAGAGCTCTATCACCACCCCAACACAAGAAACCTACAGAGAATATGATTATGACAATGGA

Alignment

ORF - retro_dord_689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 52.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEELRKSGEAKYFHLNDDLHVLIEVFAPPAEAYARMGHALEEIKKFLIPDYND-EIRQAQLQELTYLNGG
          EEELRK.GE..YFHLNDD.HVL.EVFAPPAEA.A.MGHALEEIKKFL.PDYND...RQAQLQELTYL.GG
Retrocopy EEELRKRGETRYFHLNDDFHVLTEVFAPPAEARAQMGHALEEIKKFLTPDYND<QTRQAQLQELTYLDGG

Parental  SENADVPVVRGKPTL-RTRGVATPALARGRGVTARPVGVGVPRGTPAPRGVLSTRGPVSRGRGLLTPRAR
          .ENAD.PVV.GKPTL...RGVA.....RG.......VGV..P.GTPAPRGVLST.GPVS.GRGL.TPRAR
Retrocopy AENADAPVV*GKPTL<TIRGVAR---GRGLQPSQLGVGV--PQGTPAPRGVLSTPGPVSQGRGLFTPRAR

Parental  GVPPSGYRAPPPP-PTQETYGEYDYDDG
          G.PPSGYRA..PP.PTQETY.EYDYD.G
Retrocopy GMPPSGYRALSPP<PTQETYREYDYDNG

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_689 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010878	2 retrocopies	retro_dnov_1085, retro_dnov_1131,
Dipodomys ordii	ENSDORG00000014595	1 retrocopy	retro_dord_689 ,
Equus caballus	ENSECAG00000010194	1 retrocopy	retro_ecab_460,
Otolemur garnettii	ENSOGAG00000005150	3 retrocopies	retro_ogar_2456, retro_ogar_3114, retro_ogar_550,
Sarcophilus harrisii	ENSSHAG00000000632	1 retrocopy	retro_shar_179,
Tursiops truncatus	ENSTTRG00000001270	2 retrocopies	retro_ttru_1633, retro_ttru_1929,