RetrogeneDB ID: retro_dord_77

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_2217:136358..136678(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dnajc24
• Ensembl ID: ENSDORG00000000248
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 24 [Source:MGI Symbol;Acc:MGI:1919522]

Sequence

>retro_dord_77
ATAATGGCATTTGAGCAGACACCAAAAAAGGACTGGTACAGTATTTAGGGTGCAGATCCATCTGCTGAAATGGCTGACCT
AAAACAAAAACATCAAAAACTCGTATTAATGTGCTATCTAGAAAAACAGAGTACAGATGTGCCAGCAGGAATGGCAGATG
AATATATACAGAAGCTTGCCGAAATTGAGCAGACATGGAAAATTCTAGGGAATGAAGAGACAAAAAACGAAGAGTATGAC
CTGCAGCAGATGATAATGAGCTACAAAATATGGCACCAGTAGATGATCCAGTGTATCCTGAAGAAACATCTTGGAATGAA

Alignment

ORF - retro_dord_77 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 72.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMAFKQTPKKDWYSILGADPSADVADLKQKYQKLVLMYHPDKQSTDVPAGMLEEYIQKFIEIDQAWKILG
          .MAF.QTPKKDWYSI.GADPSA..ADLKQK.QKLVLM....KQSTDVPAGM..EYIQK..EI.Q.WKILG
Retrocopy IMAFEQTPKKDWYSI*GADPSAEMADLKQKHQKLVLMCYLEKQSTDVPAGMADEYIQKLAEIEQTWKILG

Parental  NEETK-KEYDLQR-HDDELQNMGPVDAKVYLEEMSWNE
          NEETK..EYDLQ...D.ELQNM.PVD..VY.EE.SWNE
Retrocopy NEETKNEEYDLQQ<DDNELQNMAPVDDPVYPEETSWNE

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_77 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013512	1 retrocopy	retro_dnov_2247,
Dipodomys ordii	ENSDORG00000000248	3 retrocopies	retro_dord_221, retro_dord_395, retro_dord_77 ,
Echinops telfairi	ENSETEG00000003054	1 retrocopy	retro_etel_161,
Microcebus murinus	ENSMICG00000007553	3 retrocopies	retro_mmur_1052, retro_mmur_1150, retro_mmur_973,
Macaca mulatta	ENSMMUG00000006845	1 retrocopy	retro_mmul_2112,
Nomascus leucogenys	ENSNLEG00000017878	1 retrocopy	retro_nleu_3029,
Otolemur garnettii	ENSOGAG00000007848	1 retrocopy	retro_ogar_1542,
Ochotona princeps	ENSOPRG00000001638	1 retrocopy	retro_opri_881,
Pongo abelii	ENSPPYG00000003390	2 retrocopies	retro_pabe_2783, retro_pabe_2788,
Pan troglodytes	ENSPTRG00000003471	1 retrocopy	retro_ptro_2301,
Tarsius syrichta	ENSTSYG00000009243	1 retrocopy	retro_tsyr_623,