RetrogeneDB ID: retro_cfam_1433

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 31:13803837..13804438(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPS2
• Ensembl ID: ENSCAFG00000011662
• Aliases: None
• Description: phosphoribosyl pyrophosphate synthetase 2 [Source:HGNC Symbol;Acc:9465]

Sequence

>retro_cfam_1433
GCTCTTGCTGGGGCAGATCACATCATCACCATGGACCTGCATGACTCTCAGGTCCAGGGATTCTTCAACATTCCAGTGGA
TAATTTGTCTGTGGAGCCTGCAATCCTCTAGTGAATTCAGGAGAACATTGCCAAGTGGAGGAACTGTATTATCATTTACC
TGATGTGACGGGAGCTACAAGGGTCATATAAACTGCAGACAGGGTGAATATGGAATTTTCCTTCATTCACAAAGAGAGGA
AGAAAGCAAATGAAGTGGACTGGATGGTTCTGGTAAGTGGCATGAAGGACCACATGGCTATCCTCATGGAAGACATGGCT
GATATGTGTAGCACCACCTGCCATGCTGCAGACAAGCTACTCTAAGGAGCCACCAAGGCTTATGCTATTCTTACCCATGG
GATCTTCTCTGGGCCAGCTACTTCCAGAATGAATATGCTGCCTTTGAGGCTGGTGTTGTCACAGACAGCATTCTGCAAGG
TGACAAAATGAGACACTGTTCCAAGATACAGGTGATTGATATCCTTATGATCTTGGCAAAGGCAATCCCAAGGAAACACA
ATGGTGAATCTGTGTTTTACCTATTCAGCTACATCCTGCTA

Alignment

ORF - retro_cfam_1433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.57 %
• Parental protein coverage: 63.52 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLQWIRENIAEWRNCIIVS-PDAGGAKRVTSIADRL
          ..AGADHIITMDLH.SQ.QGFF.IPVDNL..EPA.L..I.ENIA.WRNCII...PD..GA.RV...ADR.
Retrocopy ALAGADHIITMDLHDSQVQGFFNIPVDNLSVEPAIL**IQENIAKWRNCIIIY<PDVTGATRVI*TADRV

Parental  NVEFALIHKERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAGATKVYAILTHGIFSG
          N.EF..IHKERKKANEVD.MVLV...KD..AIL..DMAD.C.T.CHAADKLL..GATK.YAILTHGIFSG
Retrocopy NMEFSFIHKERKKANEVDWMVLVSGMKDHMAILMEDMADMCSTTCHAADKLL-*GATKAYAILTHGIFSG

Parental  PAISRIN-NAAFEAVVVTNTIPQEDKMKHCPKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
          PA.SR.N..AAFEA.VVT..I.Q.DKM.HC.KIQVIDI.MILA.AI.R.HNGESV.YLFS...L
Retrocopy PATSRMN<YAAFEAGVVTDSILQGDKMRHCSKIQVIDILMILAKAIPRKHNGESVFYLFSYILL

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.00 RPM	6.34 RPM
SRP017611_brain	0.00 RPM	3.18 RPM
SRP017611_kidney	0.00 RPM	21.20 RPM
SRP017611_liver	0.00 RPM	6.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1433 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1433 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1433 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011662	2 retrocopies	retro_cfam_1037, retro_cfam_1433 ,
Canis familiaris	ENSCAFG00000017976	1 retrocopy	retro_cfam_1443,
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,
Tupaia belangeri	ENSTBEG00000009917	1 retrocopy	retro_tbel_1245,
Tursiops truncatus	ENSTTRG00000003226	1 retrocopy	retro_ttru_1494,