RetrogeneDB ID: retro_itri_1668

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393620.1:781253..781805(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPS2
• Ensembl ID: ENSSTOG00000006056
• Aliases: None
• Description: phosphoribosyl pyrophosphate synthetase 2 [Source:HGNC Symbol;Acc:9465]

Sequence

>retro_itri_1668
TCAGCAGCAGCTCACACCAGGACCTGTCCCAGCATGGCTGACCCCCTTGGCCTGTAGCTAGGCATGGTGGTCACCAAGGA
GTTCAGTAGCCAGGAGACCATCATTGAGCTTGGTGAAATGTGAGAGGGGAAGATGTCTATGTCATCCAGAGTGGCTGTGG
AGAAATCAATGACAACCTGATGGAACCTGCTCATCATGATCAATACCTGCAAGATTGCCTCATCATCCAGGTGACCGCAG
TGATCCTGTGTTTTCCATATGCCTGACAAGATAAAAAGGACAAGAGTCATGCTCAATTTCTGCAAAACTTGTGGCTAACA
TGCTCTCGGTTGCTGGGTCTGATCACATCATCACAATGGATCTGCATGCCTCTCGGATACAGGGATTCCTATATATTCCT
GTGGATAACTTATACATGGAGCCTGCAGTTCTGCAGTGGATTTGGAGAACATCACTGAGTAGGAGGACTATATCATGGTT
TCACTGAATCCACGGGGAGCCAAGAGGGTCACATCAATTGCAGATAGGTTGAATGTGGAATTTGCTTTGATT

Alignment

ORF - retro_itri_1668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.32 %
• Parental protein coverage: 58.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SGSSHQDLSQRVADRLGLELGKVVTKKFSNQETSVEIGE-SVRGEDVYIIQSGCGEINDNLME-LLIMIN
          S...H.......AD.LGL.LG.VVTK.FS.QET..E.GE..VRGEDVY.IQSGCGEINDNLME.LLIMIN
Retrocopy SAAAHTRTCPSMADPLGL*LGMVVTKEFSSQETIIELGE<NVRGEDVYVIQSGCGEINDNLME>LLIMIN

Parental  ACKIASSSR-VTAVIPCFPYARQDKKDKSRAP-ISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVD
          .CKIASSSR.VTAVI.CFPYA.QDKKDKS.A..ISAKLVANMLSVAG.DHIITMDLHAS.IQGF..IPVD
Retrocopy TCKIASSSR<VTAVILCFPYA*QDKKDKSHAQ<ISAKLVANMLSVAGSDHIITMDLHASRIQGFLYIPVD

Parental  NLYAEPAVLQWI-RENITEWKNCIIVSPDAGGAKRVTSIADRLNVEFALI
          NLY.EPAVLQWI..ENITE....I.VS....GAKRVTSIADRLNVEFALI
Retrocopy NLYMEPAVLQWI<LENITE*EDYIMVSLNPRGAKRVTSIADRLNVEFALI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1668 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1668 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011662	2 retrocopies	retro_cfam_1037, retro_cfam_1433,
Callithrix jacchus	ENSCJAG00000003885	1 retrocopy	retro_cjac_364,
Echinops telfairi	ENSETEG00000005166	2 retrocopies	retro_etel_1613, retro_etel_669,
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,
Otolemur garnettii	ENSOGAG00000016087	1 retrocopy	retro_ogar_1440,
Procavia capensis	ENSPCAG00000001197	2 retrocopies	retro_pcap_219, retro_pcap_292,
Pongo abelii	ENSPPYG00000020125	1 retrocopy	retro_pabe_3431,
Pteropus vampyrus	ENSPVAG00000009452	1 retrocopy	retro_pvam_1224,
Sorex araneus	ENSSARG00000007710	1 retrocopy	retro_sara_18,
Ictidomys tridecemlineatus	ENSSTOG00000006056	1 retrocopy	retro_itri_1668 ,
Ictidomys tridecemlineatus	ENSSTOG00000007638	2 retrocopies	retro_itri_11, retro_itri_173,
Tupaia belangeri	ENSTBEG00000009917	1 retrocopy	retro_tbel_1245,
Tursiops truncatus	ENSTTRG00000003226	1 retrocopy	retro_ttru_1494,