RetrogeneDB ID: retro_cfam_1037

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:34043741..34044470(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000007678
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1037
ATGCCCAACGTCGTGCTCTTCAGCGGTAGCTCGCACCAGGACCTGTCCCAGTGCGTGGCCGACCAGCTGGGCCTGGAACT
GGGCAAGGTGGTCACTAAGAAGTTCAGCAACCAGGAGACCAGCGTCGAGATCAGTGAAAGCGTGAGGGGCGAAGATGTCT
ACATCATCCAGAGTGGCTGTGGAGAAATCAATGACAACCTGATGGAGCTCCTTGTCATGATCAACGCCTGCAAGATCGCG
TCATCATCCAGGGTGACTGCCATAATCCTGTGTTTTCCATACGCCCGACAGGATAAGAAGGACAAGAGCCGAGCTCCGAT
TTCTGCGAAACTTGTGGCCAATATGCTCTGGGTCGCTGGGGCCGATCACATCATCACCATGGACCTGCATGCTTCTCAGA
TCCAGGGCTTCTTTGACACCCCGGTGGAAAACCTGTACGCGGAGCCCGCCGTCCTGCAGTGGATCCGAGAGAACGTTGCT
GAGTGGAGGAACTGTATCATTGTCTCGCCCGACGCCGGGGGAGCCAAGAGGGTCACATCGATTGCAGACAGGTTGGATGT
GGAATTCGCCTTGATTCACAAAGAGAGGGAGAAAGCAAATGAAGTGGACCGGATGGTTCTGGTGGGCGACGTGAAGGACC
GCGTGGCTATCCTCGTGGACGACATGGCTGACACCTGTGGCACCATCTGCCACGCCGCGGACAAGCTGCTCTCCGCCGGA
GCCACCAAG

Alignment

ORF - retro_cfam_1037 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.65 %
• Parental protein coverage: 76.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNIVLFSGSSHQDLSQRVADRLGLELGKVVTKKFSNQETSVEIGESVRGEDVYIIQSGCGEINDNLMEL
          MPN.VLFSGSSHQDLSQ.VAD.LGLELGKVVTKKFSNQETSVEI.ESVRGEDVYIIQSGCGEINDNLMEL
Retrocopy MPNVVLFSGSSHQDLSQCVADQLGLELGKVVTKKFSNQETSVEISESVRGEDVYIIQSGCGEINDNLMEL

Parental  LIMINACKIASSSRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDI
          L.MINACKIASSSRVTA.I.CFPYARQDKKDKSRAPISAKLVANML.VAGADHIITMDLHASQIQGFFD.
Retrocopy LVMINACKIASSSRVTAIILCFPYARQDKKDKSRAPISAKLVANMLWVAGADHIITMDLHASQIQGFFDT

Parental  PVDNLYAEPAVLQWIRENIAEWRNCIIVSPDAGGAKRVTSIADRLNVEFALIHKERKKANEVDRMVLVGD
          PV.NLYAEPAVLQWIREN.AEWRNCIIVSPDAGGAKRVTSIADRL.VEFALIHKER.KANEVDRMVLVGD
Retrocopy PVENLYAEPAVLQWIRENVAEWRNCIIVSPDAGGAKRVTSIADRLDVEFALIHKEREKANEVDRMVLVGD

Parental  VKDRVAILVDDMADTCGTICHAADKLLSAGATK
          VKDRVAILVDDMADTCGTICHAADKLLSAGATK
Retrocopy VKDRVAILVDDMADTCGTICHAADKLLSAGATK

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	0.34 RPM	6.34 RPM
SRP017611_brain	0.08 RPM	3.18 RPM
SRP017611_kidney	0.13 RPM	21.20 RPM
SRP017611_liver	0.07 RPM	6.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1037 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1037 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1037 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,