RetrogeneDB ID: retro_ocun_427

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 10:46035275..46036034(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPBP1L1
• Ensembl ID: ENSOCUG00000017939
• Aliases: None
• Description: GC-rich promoter binding protein 1-like 1 [Source:HGNC Symbol;Acc:28843]

Sequence

>retro_ocun_427
ATGGCACAGCAATGCTTTGATCCTGCTTGGAGAAATTTCTCAACACCACAGTCAGCTAATTCAACTACAGCCACCTTTGA
AAAATGCAGAGAACATCTTCCCCGAGGAGAAGGTATACTTGGAGTAACCCGCCATCGGCACAGTTCCTCTGATGGCTTTT
TTAACAATGGACTGTTACGAACTACAGATTCCTGGCACCAGCCCTCGCTGTTCCGCCCTGATTCTGTGGACTCCGGTGTC
TCTAAAGGAACACATGCTGGAATCCCAGGGAACACACCTGGTCGGCATGGCTCTTCCCGAGGTCATCGTGATGGTGTGAG
CTAGCGCAGTGGAGGTGGGCAGGGAGCCATTGGCACTGGAATGGCAGCTTGCACACCTGGAGAGGCTGTGTCTTTCAGGA
AAAGCCTCCAACAGAGATTAGGGAAGAAAAGAAAGAAGACAAGGTAGAAGAATTACAGTTTTAAGAGGATGATTTTTCTT
CTTTGAATACAGAAGCTGGCAAACAGAATCAGCCATGCAGACTTATTGGGACCCTTTCTGGAGAGTGGGGAAACCCATCT
AGTGCTGGGCAACCTTCCAAGATGTTAGTCATCAGAAAATTCCCAGAGAGGATCCTGCTGCTGCCTTCTCTGCTTCATTC
ACCTCACCAGGATCTCACCTTGCAAATGGGAACAAAGCATCAGCCATGGTTCCAAGTGCCAAAAGAAGTTGCTTCCTTAG
CCTGCACCACCTCCTTCCAAGCCCAATGCATGGAAAGCT

Alignment

ORF - retro_ocun_427 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.54 %
• Parental protein coverage: 55.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAQHDFVPAWLNFSTPQSAKSPTATFEKHREHLPRGEGRFGVSRRRHNSSDGFFNNGPLRTTDSWHQPSL
          MAQ..F.PAW.NFSTPQSA.S.TATFEK.REHLPRGEG..GV.R.RH.SSDGFFNNG.LRTTDSWHQPSL
Retrocopy MAQQCFDPAWRNFSTPQSANSTTATFEKCREHLPRGEGILGVTRHRHSSSDGFFNNGLLRTTDSWHQPSL

Parental  FRHDSVDSGVSKGAYAGITGNTSGWHGSSRGHHDGVSQRSGGG-AGNHRHWNGSLHTRKGCAFQEKPPTE
          FR.DSVDSGVSKG..AGI.GNT.G.HGSSRGH.DGVS.RSGGG.AG.H.HWNGSLHT..GC.FQEKPPTE
Retrocopy FRPDSVDSGVSKGTHAGIPGNTPGRHGSSRGHRDGVS*RSGGG<AGSHWHWNGSLHTWRGCVFQEKPPTE

Parental  IREEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRPIGTLSGVWENPPSAKQPSKMLVIK-KISKEDPAA
          IREEKKEDKVE.LQF.E.DF.SLN.EAGKQNQPCR.IGTLSG.W.NP.SA.QPSKMLVI..KI..EDPAA
Retrocopy IREEKKEDKVEELQF*EDDFSSLNTEAGKQNQPCRLIGTLSGEWGNPSSAGQPSKMLVIR<KIPREDPAA

Parental  AFSAAFTSPGSHHANGNKASTMVPSV-YKNLVPKPAPPPSKPNAWKA
          AFSA.FTSPGSH.ANGNKAS.MVPS...K.L.P.PAPPPSKPNAWKA
Retrocopy AFSASFTSPGSHLANGNKASAMVPSA<QKKLLP*PAPPPSKPNAWKA

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	41.89 RPM
SRP017611_kidney	0.00 RPM	65.78 RPM
SRP017611_liver	0.00 RPM	44.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_427 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_427 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_427 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010454	1 retrocopy	retro_chof_53,
Microcebus murinus	ENSMICG00000008449	1 retrocopy	retro_mmur_164,
Myotis lucifugus	ENSMLUG00000012432	2 retrocopies	retro_mluc_211, retro_mluc_834,
Mus musculus	ENSMUSG00000034042	2 retrocopies	retro_mmus_1391, retro_mmus_405,
Oryctolagus cuniculus	ENSOCUG00000017939	1 retrocopy	retro_ocun_427 ,
Otolemur garnettii	ENSOGAG00000004134	1 retrocopy	retro_ogar_1859,
Ochotona princeps	ENSOPRG00000001584	1 retrocopy	retro_opri_928,
Rattus norvegicus	ENSRNOG00000037595	1 retrocopy	retro_rnor_390,
Ictidomys tridecemlineatus	ENSSTOG00000013491	1 retrocopy	retro_itri_243,