RetrogeneDB ID: retro_cfam_1739

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:48647979..48648562(+)
• Located in intron of: ENSCAFG00000023117

Retrocopy information

• Ensembl ID: ENSCAFG00000018860
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRDX2
• Ensembl ID: ENSCAFG00000017163
• Aliases: None
• Description: peroxiredoxin 2 [Source:HGNC Symbol;Acc:9353]

Sequence

>retro_cfam_1739
ATGACCTCTGGCAAGGCACACATCGGAAAGCCCATTGCGCCTTTCCAGGTCACTGCTGTGGTGGACAGCATCTTCAAGGA
GGCGAAGCTTTGCAACTACAAAGGGAAATACTTGGTCCCCTTTTTCTACCCGTTGGACATCACCTTCGTCTGCCCAATGG
AGATTACTGGCTTTAGCGAGCATGCCAAAGACTTCGGCAAGCTGCGCTGTGAGATGCTGGGGTCTCCGTGGACTCTCAGT
TCACCCACCTGCTTGGATCAACACTCCCAGGAAGGACGGAGGCCCCCTGAACATCCCCTGCTGGCTGCGTAACTAGAAGT
TTATCCGAAGATTATGGTGTGCTGAAGGAAGATGAGGGCATTGCCTACAGGGGCCTCTTTATCATCGATGGCAAGGTGTC
CCTCTCCAGATCACTGTCAATGATTTGTCTGTGGGGCACTCTGTGGATGAAGTTCTGCAACTGATTCAGGCCTTGCAGTA
CACGGATGAGCACAGGGAAGTCTACCCGCCTGGCTGGAAGCCAGGCAGTGACACAATCAAGCCTAACATGGACGACAGCA
AAGAATACTTCTCCAAACACAAC

Alignment

ORF - retro_cfam_1739 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MTSGKAHIGKPAPPFQATAVVDGAFKEVKLCDYKGKYLVLFFYPLDFTFVCPTEIIAFSEHAEDFRKLGC
          MTSGKAHIGKP..PFQ.TAVVD..FKE.KLC.YKGKYLV.FFYPLD.TFVCP.EI..FSEHA.DF.KL.C
Retrocopy MTSGKAHIGKPIAPFQVTAVVDSIFKEAKLCNYKGKYLVPFFYPLDITFVCPMEITGFSEHAKDFGKLRC

Parental  EVLG-VSVDSQFTHL-AWINTPRKEGGLGPLNI-PLVAD-VTRSLSEDYGVLKEDEGIAYRGLFIIDGK-
          E.LG.VSVDSQFTHL.AWINTPRK.GG..PLNI.PL.A..VTRSLSEDYGVLKEDEGIAYRGLFIIDGK.
Retrocopy EMLG<VSVDSQFTHL<AWINTPRKDGG--PLNI<PLLAA<VTRSLSEDYGVLKEDEGIAYRGLFIIDGK<

Parental  GVLRQITVNDLPVGRSVDEVLRLVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSKHN
          GV..QITVNDL.VG.SVDEVL.L.QA.QYTDEH.EV.P.GWKPGSDTIKPN.DDSKEYFSKHN
Retrocopy GVPLQITVNDLSVGHSVDEVLQLIQALQYTDEHREVYPPGWKPGSDTIKPNMDDSKEYFSKHN

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	312.47 RPM
SRP017611_brain	0.00 RPM	142.75 RPM
SRP017611_kidney	0.00 RPM	112.26 RPM
SRP017611_liver	0.07 RPM	5.08 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1739 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1739 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1739 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012307	3 retrocopies	retro_amel_1188, retro_amel_1710, retro_amel_55,
Canis familiaris	ENSCAFG00000004567	5 retrocopies	retro_cfam_1313, retro_cfam_270, retro_cfam_577, retro_cfam_834, retro_cfam_988,
Canis familiaris	ENSCAFG00000012109	3 retrocopies	retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Canis familiaris	ENSCAFG00000017163	3 retrocopies	retro_cfam_1603, retro_cfam_1624, retro_cfam_1739 ,
Ciona intestinalis	ENSCING00000003002	1 retrocopy	retro_cint_8,
Callithrix jacchus	ENSCJAG00000004882	4 retrocopies	retro_cjac_1269, retro_cjac_1795, retro_cjac_2356, retro_cjac_2392,
Dipodomys ordii	ENSDORG00000009005	1 retrocopy	retro_dord_176,
Felis catus	ENSFCAG00000000473	1 retrocopy	retro_fcat_1755,
Homo sapiens	ENSG00000167815	3 retrocopies	retro_hsap_1184, retro_hsap_3278, retro_hsap_3500,
Gorilla gorilla	ENSGGOG00000025089	3 retrocopies	retro_ggor_2366, retro_ggor_2833, retro_ggor_923,
Macaca mulatta	ENSMMUG00000005689	2 retrocopies	retro_mmul_1780, retro_mmul_2061,
Monodelphis domestica	ENSMODG00000006978	1 retrocopy	retro_mdom_1770,
Mustela putorius furo	ENSMPUG00000004591	2 retrocopies	retro_mputfur_28, retro_mputfur_660,
Mus musculus	ENSMUSG00000005161	2 retrocopies	retro_mmus_2403, retro_mmus_472,
Nomascus leucogenys	ENSNLEG00000012800	2 retrocopies	retro_nleu_2110, retro_nleu_2883,
Otolemur garnettii	ENSOGAG00000024998	2 retrocopies	retro_ogar_1993, retro_ogar_244,
Pongo abelii	ENSPPYG00000009607	3 retrocopies	retro_pabe_2711, retro_pabe_2892, retro_pabe_988,
Pan troglodytes	ENSPTRG00000010541	3 retrocopies	retro_ptro_2217, retro_ptro_2372, retro_ptro_812,
Rattus norvegicus	ENSRNOG00000003520	2 retrocopies	retro_rnor_2288, retro_rnor_497,
Sorex araneus	ENSSARG00000000146	1 retrocopy	retro_sara_96,
Sarcophilus harrisii	ENSSHAG00000015596	1 retrocopy	retro_shar_305,
Sus scrofa	ENSSSCG00000013736	2 retrocopies	retro_sscr_155, retro_sscr_962,
Ictidomys tridecemlineatus	ENSSTOG00000025862	1 retrocopy	retro_itri_842,