RetrogeneDB ID: retro_ocun_1202

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:98596667..98597589(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGFG2
• Ensembl ID: ENSOCUG00000008631
• Aliases: None
• Description: ArfGAP with FG repeats 2 [Source:HGNC Symbol;Acc:5177]

Sequence

>retro_ocun_1202
GGGAAACCCGTGTGATCACTTCTGGGTGATCCTGTGTCTCGCTCAACTGCAGCCTCCACCTAGAGCCAGTCTGTCCAACA
GTCTCAGCCCTGGACGGCCTAGGTTCACTCTGTCGGGAAAGCCAATATAGACTTGCTGGTCTACCCTGGGGAGACTTCCT
TGCTGCTCCCCAGGCTGTCCCAGTCTTTGCTCTGTTCCCAGCCTTGGGGTGCCAGATGCCTCCCTTTGGGGGTTTTGCCA
ATTTTTATGCCTTTGGAAGCAGCCGCAACCCTGCTGTGTTTGGAAGTACCCTTCCAGCAGGCCAGACCCCATTCCATGGC
CAGGCCACATCCACAGCTACTCATATGCTAACCGCAATAGCTTTGGGAGCAGCCAAGTGACTACATTGGGACCATTACTT
TGGCACCTGTCAGTCAGGCAAACAGCCTCAGAGAGGTAGATAGCCTCCTGGGCTCTGGTACATTGGCTGGAGGTGTCCCT
GACAGAATCATCGGGATGACTGACCAGGTCCCCACACTACAATCTGCTACAACTGGAGGCAGCAGAAGCCCAGGGTTTGC
CTTTGGAGGCCTCATCAGCCTGGTCCCTGTCCCTGCTGCCCAGCCCGGGCAACCTTCCACCATCTGGTTCCAGCTCAATG
GCCTAGCCCCACGGTCCAATTATGGGATGAGCAGCGTGGGCCTTGCTTCCCCCAGATAGCGCCATCTGCTGGGCCCTTTG
CCAGTCCTTCCCGACCCAGCTGTTGACTGCACAGTGCTCACTGGCTCAGCAGGAGAATGGCTCTTCCTTTGGGCACATAG
AATCAGCCAAGCTGAGGCAGAGGTCCCTGAGCCAGCCAGCCCAGATCTCCACCAATCCCTTTGTGGCTAAACCCTCATCA
AGCCCATTTGTCTCCAAACCTTCAACCACCCACCCATGTCTA

Alignment

ORF - retro_ocun_1202 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.28 %
• Parental protein coverage: 63.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GDPVPSLSAAASTSSQSVSQSQARTAQARSSQLPAHSAVKKATTDLLADIG-GDPFAAPQAAPAFAPFPA
          G.PV.SL.......S...S.......Q........HS.V.KA..DLL...G.GD..AAPQA.P.FA.FPA
Retrocopy GKPV*SLLGDPVSRSTAAST*SQSVQQSQPWTA*VHS-VGKANIDLLVYPG<GDFLAAPQAVPVFALFPA

Parental  FGGHTPSPGGFANFDAFGSSPGAAVFGSVPPAGQAPFPAQPTPAASRMLTGSFSFG-SSQVTP-FGTTPL
          .G...P..GGFANF.AFGSS...AVFGS..PAGQ.PF..Q.T..A..MLT.....G.SSQVT...GT..L
Retrocopy LGCQMPPFGGFANFYAFGSSRNPAVFGSTLPAGQTPFHGQATSTATHMLT-AIALG<SSQVTT<IGTITL

Parental  APASQPNSLAEVGSLLGPGASAGGVPGSIFGMTGQVPT----ASGGS-SPGLAFGGLTNPFAAPAAQPRL
          AP.SQ.NSL.EV.SLLG.G..AGGVP..I.GMT.QVPT......GGS.SPG.AFGGL......PAAQP..
Retrocopy APVSQANSLREVDSLLGSGTLAGGVPDRIIGMTDQVPTLQSATTGGSRSPGFAFGGLISLVPVPAAQPGQ

Parental  PSTNPFQSNGLAPGPGFGMSSV-GPGFPQTVPPAGTFASP-FPAPLFPPQSSLAQQENGTSFGDLGSAKL
          PST..FQ.NGLAP....GMSSV.GP.FPQ..P.AG.FASP.FP..L...Q.SLAQQENG.SFG...SAKL
Retrocopy PSTIWFQLNGLAPRSNYGMSSV<GPCFPQIAPSAGPFASP<FPTQLLTAQCSLAQQENGSSFGHIESAKL

Parental  GQRPLSQPAGISTNPFMTGSSPSPFATKPPTTNPFL
          .QR.LSQPA.ISTNPF....S.SPF..KP.TT.P.L
Retrocopy RQRSLSQPAQISTNPFVAKPSSSPFVSKPSTTHPCL

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
SRP017611_brain	0.00 RPM	42.11 RPM
SRP017611_kidney	0.00 RPM	94.67 RPM
SRP017611_liver	0.00 RPM	37.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1202 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1202 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1202 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000008631	1 retrocopy	retro_ocun_1202 ,