RetrogeneDB ID: retro_dord_223

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_5978:137284..137812(+)
• Located in intron of: ENSDORG00000000354

Retrocopy information

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

Parental gene information

• Parental gene symbol: Prps2
• Ensembl ID: ENSDORG00000007577
• Aliases: None
• Description: phosphoribosyl pyrophosphate synthetase 2 [Source:MGI Symbol;Acc:MGI:97776]

Sequence

>retro_dord_223
ATGCCAAATATCAAAATCTTCAGCAATAGCTCCTACCACGATTAACTTCAGAAAAATGCTGACCACCTGGGCCTGAAGCT
AAGCAAGGTGGTAATTAAGAAATTCAGCAGTCAGGAGACCTGTGTAGGAATTGGTGAAAGTGTATGTGGAGAAGATGTCT
ACATTGTTCAGAGTGGTTGTGGTGAAATTAATGACAATCTAATGGTGCTTTTGATCATGATTAAAGCCTATAAGATTGCT
TCACCCAGCCAAGATTCTGCAGTCATCCCATGTTTTCCATATGCTCAGCAGGATAAGAAGTCTAACAGCCGAGCTCCAAT
CTCAGCCAAGCTGATTGCAAATATGCTGTCTGTAGCTGGAGCAGATCACATCATCACAATGGATCTACATGCCTCTCAGA
TTCAGGGCTTTTTTGATATCCCATTGGACAATTTGTATGCAGAACCTGCTGTCCTAAAGTGGATTAGGGAGAACATCTCT
GAATGGAGAAACTGTGCTATTGTTTCACCTGATACAGGCAGAGCCAAG

Alignment

ORF - retro_dord_223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.33 %
• Parental protein coverage: 55.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNIVLFSGSSHQDLSQRVADRLGLELGKVVTKKFSNQETSVEIGESVRGEDVYIIQSGCGEINDNLMEL
          MPNI..FS.SS..D..Q..AD.LGL.L.KVV.KKFS.QET.V.IGESV.GEDVYI.QSGCGEINDNLM.L
Retrocopy MPNIKIFSNSSYHD*LQKNADHLGLKLSKVVIKKFSSQETCVGIGESVCGEDVYIVQSGCGEINDNLMVL

Parental  LIMINACKIASSSRVTAVIPCFPYARQDKKDKVGESRAPISAKLVANMLSVAGADHIITMDLHASQIQGF
          LIMI.A.KIAS.S...AVIPCFPYA.QDKK.....SRAPISAKL.ANMLSVAGADHIITMDLHASQIQGF
Retrocopy LIMIKAYKIASPSQDSAVIPCFPYAQQDKKSN---SRAPISAKLIANMLSVAGADHIITMDLHASQIQGF

Parental  FDIPVDNLYAEPAVLQWIRENISEWRNCIIVSPDAGGAK
          FDIP.DNLYAEPAVL.WIRENISEWRNC.IVSPD.G.AK
Retrocopy FDIPLDNLYAEPAVLKWIRENISEWRNCAIVSPDTGRAK

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_223 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007206	1 retrocopy	retro_cpor_16,
Dipodomys ordii	ENSDORG00000007577	2 retrocopies	retro_dord_223 , retro_dord_605,
Dipodomys ordii	ENSDORG00000014534	2 retrocopies	retro_dord_356, retro_dord_632,
Felis catus	ENSFCAG00000026323	1 retrocopy	retro_fcat_527,
Monodelphis domestica	ENSMODG00000017334	4 retrocopies	retro_mdom_1323, retro_mdom_1359, retro_mdom_258, retro_mdom_834,
Sorex araneus	ENSSARG00000007710	1 retrocopy	retro_sara_18,