RetrogeneDB ID: retro_dord_688

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_5563:45633..45993(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nucks1
• Ensembl ID: ENSDORG00000003183
• Aliases: None
• Description: nuclear casein kinase and cyclin-dependent kinase substrate 1 [Source:MGI Symbol;Acc:MGI:1934811]

Sequence

>retro_dord_688
AATAGAAAGGTCGTTGATTATTCACAGTTTCAGGAATCTGATGATGCAGATGAAGATTATGGAAGAGATTCCGGCCCTCC
TGCTAAGAAAATTTGATCATCTCCTCGAGAAGCTAAAAATAAGAGGAGATCTGGAAAGAATTCACAGGAAGATAGTGAGG
ACTCAGAAGAAAAAGATGTGAAGACCAAGAAGGATGATTCTCATTCAGCAGAGGAGAATGAAGATGAAAAAGAAGATCAT
AGAAATGTGCGCCAGCAACGACAGGCAGCATCTAAGACAGCTTCTAAACAGAGAGAGATGCTCATGGAAGATGTTGGCAG
TGAGGAGGAACCAGAAGAAGATGAGGCACCATTGCAGGAG

Alignment

ORF - retro_dord_688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.51 %
• Parental protein coverage: 51.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NRKVVDYSQFQESDDADEDYGRDSGPPAKKIRSSPREAKNKRRSGKNSQEDXXXXXXXXXXXXXXXXXXX
          NRKVVDYSQFQESDDADEDYGRDSGPPAKKI.SSPREAKNKRRSGKNSQED...................
Retrocopy NRKVVDYSQFQESDDADEDYGRDSGPPAKKI*SSPREAKNKRRSGKNSQEDSEDSEEKDVKTKKDDSHSA

Parental  XESEDEKEDHKNVRQQRQAASKAASKQREMLMEDVGSEEEPEEEDEAPFQE
          .E.EDEKEDH.NVRQQRQAASK.ASKQREMLMEDVGSEEEP.EEDEAP.QE
Retrocopy EENEDEKEDHRNVRQQRQAASKTASKQREMLMEDVGSEEEP-EEDEAPLQE

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_688 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012950	1 retrocopy	retro_amel_339,
Bos taurus	ENSBTAG00000008001	1 retrocopy	retro_btau_541,
Choloepus hoffmanni	ENSCHOG00000001855	1 retrocopy	retro_chof_437,
Dasypus novemcinctus	ENSDNOG00000017212	2 retrocopies	retro_dnov_348, retro_dnov_6,
Dipodomys ordii	ENSDORG00000003183	1 retrocopy	retro_dord_688 ,
Homo sapiens	ENSG00000069275	1 retrocopy	retro_hsap_521,
Gorilla gorilla	ENSGGOG00000026655	1 retrocopy	retro_ggor_480,
Macropus eugenii	ENSMEUG00000007829	2 retrocopies	retro_meug_2015, retro_meug_372,
Macaca mulatta	ENSMMUG00000005645	1 retrocopy	retro_mmul_422,
Monodelphis domestica	ENSMODG00000001832	1 retrocopy	retro_mdom_980,
Nomascus leucogenys	ENSNLEG00000014564	1 retrocopy	retro_nleu_2576,
Pan troglodytes	ENSPTRG00000001904	1 retrocopy	retro_ptro_389,
Rattus norvegicus	ENSRNOG00000047287	2 retrocopies	retro_rnor_2337, retro_rnor_2338,
Tupaia belangeri	ENSTBEG00000015641	1 retrocopy	retro_tbel_2591,
Tarsius syrichta	ENSTSYG00000000910	1 retrocopy	retro_tsyr_987,
Vicugna pacos	ENSVPAG00000003751	1 retrocopy	retro_vpac_313,