RetrogeneDB ID: retro_cfam_455

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:27724033..27725119(-)
• Located in intron of: ENSCAFG00000001434

Retrocopy information

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

Parental gene information

• Parental gene symbol: EGLN2
• Ensembl ID: ENSCAFG00000005079
• Aliases: None
• Description: egl nine homolog 2 (C. elegans) [Source:HGNC Symbol;Acc:14660]

Sequence

>retro_cfam_455
CAGCCACAGCCCCTAAGTCAGGCTCTTCCTTAGTTGCCAAATCCTGTGTCACCACCGTGGGATCCTGGCTGGGCCAGAAC
TGGAATGGAGAGTTACCTGCCCTATTCCCTAGTATCCTCCTACAACCAACCAGGAGCACCTGCTGAGGCCTCGGCAGGCA
GTGGGACCCCCAAGGCCACAGCCATTTCCAAAATAGCCAGCCCCCTGTGCTAGGGCTTCAGTAGGCAGAAGGATGGTCAG
TTGCAACCACTGTAGAGTAAGGGCATTGCAACACTAGTCATGAAGGGGTGCTAGCAACTGGTGGCCCAGGGTACCAGGGC
TGAGGTTCCCAAATGGAAATGGACAGAGGATGGTGGGGATGCCCCTGCACCTAAGCAAGCAACCCTTGTCTCAGGCAGTA
GAACCAGGAGGCAGAGGCCAAAGGGGAGGACACCATGGCTGTAGCAGTGGCAATGGTGAAGTCAGTGTGGGGCTAAAGGA
GAGAGTGCTGCTTACTGCATTCAAGCACCCGGCCCTGGACTATATTGTGCTCTGTATGCTGTACTACAGCATCTGTGTCA
AGGACAGCTTCCTGAGGGTGGCACTGGGTGGCCATGTGCTGGCCAAGGTAGAGACCCTGAAGTGGACTGGGCACTGGTGT
GACAGGCAGATAGGGAGCCAGCAGGCTATCCCACCACATAGCATCTGCAGGGCCAGACTGCCTAGGTAGAAGGTCACGAG
CCCAGCTGCCAAAGCATTGGGGTCCTCATAGCCCATGTGGACATGGTAATCCACCACTGCACGGAGTACTGGGTGACCGT
ATCATCAAGAGGCACACCAAGGCCATGGTGGTATCTTACTCAGGCAATAGGCTGGAGTGCATAAGGCATATGGACAATCC
CCACAGCAATGGGCACTGTATCACCTCTATCTATTACTTGAATCAGAACTGGGACATCAAGGTGCATGGCAGCCTGTTGT
AGATCTCCCTGAGGCTGGCCCATGATAACCAACATCAAGCCACTCTTTGATGGGTTGCTCATTTTCTGGTCTGACCAGTA
GAACCCCCATGAGGTGGCACCACAGGTATGCCATCACTATCTGGTA

Alignment

ORF - retro_cfam_455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.41 %
• Parental protein coverage: 89.63 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QPQPLSQALPQLPGSVSEPLEPGRARMGVESYLPCPLLPSYHRPGAPGEASAGSGTPRATATSTTASPLR
          QPQPLSQALP.LP..VS.P..PG.AR.G.ESYLP..L..SY..PGAP.EASAGSGTP.ATA.S..ASPL.
Retrocopy QPQPLSQALP*LPNPVSPPWDPGWARTGMESYLPYSLVSSYNQPGAPAEASAGSGTPKATAISKIASPLC

Parental  EGFGGQDGGELRPLQSEGAAALVTKGCQRLAAQGARPEAPKRKWAEDGGDAPAP-SKRSWARQENREAEA
          .GF..Q..G.L.PL.S.G.A.LV.KGC..L.AQG.R.E.PK.KW.EDGGDAPAP.SK.............
Retrocopy *GFSRQKDGQLQPL*SKGIATLVMKGC*QLVAQGTRAEVPKWKWTEDGGDAPAP>SKQPLSQAVEPGGRG

Parental  EGEGGMGCSSGNGEASVGPREEVLPAAPERLALDYIVPCMRYYGICVKDSFLGAALGGCVLAEVEALKRS
          ...G..GCSSGNGE.SVG..E.VL..A....ALDYIV.CM.YY.ICVKDSFL..ALGG.VLA.VE.LK..
Retrocopy QRGGHHGCSSGNGEVSVGLKERVLLTAFKHPALDYIVLCMLYYSICVKDSFLRVALGGHVLAKVETLKWT

Parental  GRLRDGQLVSQRAIPPRSI-RGDQIAWVEGHEPGCRSIGVLMAHVDAVIRHCA-GRLGGYVINGRTKAMV
          G...D.Q..SQ.AIPP.SI....Q.A.VEGHEP.C.SIGVL.AHVD.VI.HC..G.LG...I...TKAMV
Retrocopy GHWCDRQIGSQQAIPPHSI<LQGQTA*VEGHEPSCQSIGVLIAHVDMVIHHCT<GVLGDRIIKRHTKAMV

Parental  ACYPGNGLGYVRHVDNPHGDGRCITCIYYLNQNWDVKVHGGLLQI-FPE-GRPVVANIEPLFDRLLIFWS
          ..Y.GN.L...RH.DNPH..G.CIT.IYYLNQNWD.KVHG.LL.I..PE.G.P...NI.PLFD.LLIFWS
Retrocopy VSYSGNRLECIRHMDNPHSNGHCITSIYYLNQNWDIKVHGSLL*I<LPE<GWPMITNIKPLFDGLLIFWS

Parental  DRRNPHEVKPAYATRYAI
          D..NPHEV.P.....Y..
Retrocopy DQ*NPHEVAPQVCHHYLV

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	57.20 RPM
SRP017611_brain	0.00 RPM	42.16 RPM
SRP017611_kidney	0.13 RPM	26.55 RPM
SRP017611_liver	0.00 RPM	34.95 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_455 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_455 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005079	1 retrocopy	retro_cfam_455 ,
Callithrix jacchus	ENSCJAG00000014887	1 retrocopy	retro_cjac_3275,
Felis catus	ENSFCAG00000024463	1 retrocopy	retro_fcat_1618,