RetrogeneDB ID: retro_dord_234

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6208:19979..20621(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pigf
• Ensembl ID: ENSDORG00000006083
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class F [Source:MGI Symbol;Acc:MGI:99462]

Sequence

>retro_dord_234
AGTGATATCAAGAAGCTATCTTATATGCATCTTTTGTGCATATTTTCCATTATCCTAAGCACCTTCATTCCATCATTCTT
CTTGGAGAACTTTTCAGTATTAGAAACTCACTTACTGTGGTTGTGCATGTGCTCTGTTTCTGTAACTGCCGTCAATCTCC
TATTATACTTCGTAGTGAAACCAAATGTATCCTCTAAAAGTTCACTGTGTATAAGGTAGCCAAAATTTTTTAATGCTGTA
TCGACTTTTTAATATCTTGTCTTCCTTTATGTGATTTTTGTTCTCTGTGGAGTGCCATTATTAGAGCTGGTGTTGGAAAC
ATTTTCACTTGCAGTTATTTTGTCTACTTTTACTGTTGTACCTTGTTTTTGTTTACTAGGACCAAACCTGAAAGCATGGC
TAAGAGTTTTCAGTAAAAATGGAGTTGATTCCATTTGGGAGAAGAGTCTCCAGATCACTACTATTTCTAGTTTTGTAGGA
GCATAGCTTGGAGCATTTCCTATCCCACTGGATTGGGAAAGACCATGGCAGGTATAACCCATCTCCTGTACACTTGGAGC
GACCTTTGGCTACATGGCTGGCTTAATCATTTCACCACTCTGGATATACTGGAATAGAAAGCAACTGACATATAAGAACA
AT

Alignment

ORF - retro_dord_234 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.72 %
• Parental protein coverage: 98.63 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDIKKLFYMHLLCIFSIILSTFIPSFFLENFSVLETHLLWLCICSVSVTAINLLLYFVVKPNVSSKRSSL
          SDIKKL.YMHLLCIFSIILSTFIPSFFLENFSVLETHLLWLC.CSVSVTA.NLLLYFVVKPNVSSK.SSL
Retrocopy SDIKKLSYMHLLCIFSIILSTFIPSFFLENFSVLETHLLWLCMCSVSVTAVNLLLYFVVKPNVSSK-SSL

Parental  SYKVARFLKCCIYFLISCLFLHVIFVLYGAPLLELVLETFSFAVILSTFTVVPCLCLLGPNLKAWLRVFS
          ......F......F.....FL.VIFVL.G.PLLELVLETFS.AVILSTFTVVPC.CLLGPNLKAWLRVFS
Retrocopy CIR*PKFFNAVSTF*Y-LVFLYVIFVLCGVPLLELVLETFSLAVILSTFTVVPCFCLLGPNLKAWLRVFS

Parental  KNGVNSIWENSLQITTISSFVGAWLGAFPIPLDWERPWQVWPISCTLGATFGYVAGLFISPFWIYWNRKQ
          KNGV.SIWE.SLQITTISSFVGA.LGAFPIPLDWERPWQV.PISCTLGATFGY.AGL.ISP.WIYWNRKQ
Retrocopy KNGVDSIWEKSLQITTISSFVGA*LGAFPIPLDWERPWQV*PISCTLGATFGYMAGLIISPLWIYWNRKQ

Parental  LTYKNN
          LTYKNN
Retrocopy LTYKNN

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_234 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 20 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028483	1 retrocopy	retro_acar_103,
Callithrix jacchus	ENSCJAG00000000680	2 retrocopies	retro_cjac_4146, retro_cjac_481,
Dasypus novemcinctus	ENSDNOG00000007278	2 retrocopies	retro_dnov_1980, retro_dnov_502,
Dasypus novemcinctus	ENSDNOG00000025474	1 retrocopy	retro_dnov_602,
Dipodomys ordii	ENSDORG00000006083	1 retrocopy	retro_dord_234 ,
Homo sapiens	ENSG00000151665	3 retrocopies	retro_hsap_3277, retro_hsap_4217, retro_hsap_4801,
Gorilla gorilla	ENSGGOG00000024478	3 retrocopies	retro_ggor_2229, retro_ggor_2825, retro_ggor_2988,
Myotis lucifugus	ENSMLUG00000008686	1 retrocopy	retro_mluc_1471,
Macaca mulatta	ENSMMUG00000005389	2 retrocopies	retro_mmul_1173, retro_mmul_2559,
Monodelphis domestica	ENSMODG00000000968	1 retrocopy	retro_mdom_1771,
Mustela putorius furo	ENSMPUG00000012037	1 retrocopy	retro_mputfur_810,
Nomascus leucogenys	ENSNLEG00000016924	3 retrocopies	retro_nleu_1115, retro_nleu_1455, retro_nleu_2882,
Oryctolagus cuniculus	ENSOCUG00000001130	1 retrocopy	retro_ocun_618,
Otolemur garnettii	ENSOGAG00000026734	1 retrocopy	retro_ogar_1699,
Pongo abelii	ENSPPYG00000012438	3 retrocopies	retro_pabe_2710, retro_pabe_3450, retro_pabe_3733,
Pan troglodytes	ENSPTRG00000011895	2 retrocopies	retro_ptro_2863, retro_ptro_3192,
Ictidomys tridecemlineatus	ENSSTOG00000001373	1 retrocopy	retro_itri_989,
Tupaia belangeri	ENSTBEG00000000891	1 retrocopy	retro_tbel_3809,
Tarsius syrichta	ENSTSYG00000002842	3 retrocopies	retro_tsyr_1497, retro_tsyr_1556, retro_tsyr_1820,
Vicugna pacos	ENSVPAG00000000314	1 retrocopy	retro_vpac_478,