RetrogeneDB ID: retro_dord_356

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_13582:32045..32603(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Prps1l1
• Ensembl ID: ENSDORG00000014534
• Aliases: None
• Description: phosphoribosyl pyrophosphate synthetase 1-like 1 [Source:MGI Symbol;Acc:MGI:1922706]

Sequence

>retro_dord_356
AGCCGCGCGCCCATCTCGGCGAAGCTGGTGGCCAACATGCTGTCCATCGCAGGCGCCGACCACATCATCACCATGGACCT
GCACGCGTCTCAGATTCAGGGCTTTTTCGACATCCCCGTCGACAATTTGTACGCTGAGCCAGCTGTGCTCAAGTGGGTGC
AGGAGAACATTGCCGAATGGAGGGACTGCACCGTCGTGTCTCCGGACGCGGGCGGAGCCAAGAGGGTCACCTCCATTGCC
GACCGCCTGAATGTGGACTTTGCCTTGATTCACAAAGAACGCAAGAAGGCCAACGAAGTGGACCGCATGGTGCTGGTGGG
CGACGTGAAGGACCGGGTGGCCATCCTTGTGGATGACATGGCTGACACCTGTGGGACAATCTGCCATGCAGCTGACAAAT
TAGTCTCCGCAGGAGCCACCAGCGTGTATGCCATCTTGACTCACGGAATCTTTTCTGGCCCAGCCATCGCTCGCATCAAT
AGTGCATGCTTTGAAGCAGTCGTGGTCACCAATACCATACCTCAGGAGGAGAAGATGAAGCAGTGCCCCAAGATACAG

Alignment

ORF - retro_dord_356 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.01 %
• Parental protein coverage: 89.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIRENISEWRNCTIVSPDA
          SRAPISAKLVANMLS.AGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKW..ENI.EWR.CT.VSPDA
Retrocopy SRAPISAKLVANMLSIAGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWVQENIAEWRDCTVVSPDA

Parental  GGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAGAT
          GGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAADKL.SAGAT
Retrocopy GGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLVSAGAT

Parental  RVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDKMKHCSKIQ
          .VYAILTHGIFSGPAI.RIN.ACFEAVVVTNTIPQE.KMK.C.KIQ
Retrocopy SVYAILTHGIFSGPAIARINSACFEAVVVTNTIPQEEKMKQCPKIQ

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_356 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002028	2 retrocopies	retro_dnov_2677, retro_dnov_947,
Dipodomys ordii	ENSDORG00000007577	2 retrocopies	retro_dord_223, retro_dord_605,
Dipodomys ordii	ENSDORG00000014534	2 retrocopies	retro_dord_356 , retro_dord_632,
Macropus eugenii	ENSMEUG00000010071	2 retrocopies	retro_meug_1612, retro_meug_443,
Oryctolagus cuniculus	ENSOCUG00000012391	3 retrocopies	retro_ocun_430, retro_ocun_867, retro_ocun_912,
Ochotona princeps	ENSOPRG00000013140	1 retrocopy	retro_opri_704,