RetrogeneDB ID: retro_dord_605

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_39718:6670..7197(+)
• Located in intron of: None

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_605
ATGCTGAATATAAAAATCTTCAGCGGTAGCTCCCACCAAGACTTATCTCAGAAAATTGCTGACCGCTTGGGCCTGGAGCT
AGGCAAGGTGGTGACTAAGAAATTCAGCAATCAGGAGACATGTGTGGAAATTGGTGAAACTGTACGTGAAGAAGATGTCT
ACATTGTTCAGAGTGGTTGTGGTGAAATTAATGACAATCTAATGGGGCTTTTGATCATGGTTAATGCCTGTAAGATTGCT
TCAGCCAGCCGAGTTACTGCAGTCATCCCATGCTTTCCATATGCTCAGCGGATAAGAAGGATAAGTGCCGGGCTCCAATC
TCAGCCAAGCTGGTTGCAAATACGCTGTCTGTCTCTGGTGCAGATCACATCATCACCATGGATCTACATGCTTCTCAGAT
TCAGGGCTTTTTTGATATCCCAGTGGACAATTTGTATGCAGAGCCTGCTGTCCTGAAGTGGATTAGGGAGAATATCTCTG
AATGGAGGAACTGCACTATTGTTTCACCGGATGCAGGTAGAGCCAAG

Alignment

ORF - retro_dord_605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 55.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPNIVLFSGSSHQDLSQRVADRLGLELGKVVTKKFSNQETSVEIGESVRGEDVYIIQSGCGEINDNLMEL
          M.NI..FSGSSHQDLSQ..ADRLGLELGKVVTKKFSNQET.VEIGE.VR.EDVYI.QSGCGEINDNLM.L
Retrocopy MLNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGETVREEDVYIVQSGCGEINDNLMGL

Parental  LIMINACKIASSSRVTAVIPCFPYARQ-DKKDKVGESRAPISAKLVANMLSVAGADHIITMDLHASQIQG
          LIM.NACKIAS.SRVTAVIPCFPYA...DKKDK....RAPISAKLVAN.LSV.GADHIITMDLHASQIQG
Retrocopy LIMVNACKIASASRVTAVIPCFPYAQR<DKKDK---CRAPISAKLVANTLSVSGADHIITMDLHASQIQG

Parental  FFDIPVDNLYAEPAVLQWIRENISEWRNCIIVSPDAGGAK
          FFDIPVDNLYAEPAVL.WIRENISEWRNC.IVSPDAG.AK
Retrocopy FFDIPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGRAK

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_605 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,