RetrogeneDB ID: retro_ocun_1133

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 20:8048622..8049256(+)
• Located in intron of: ENSOCUG00000004745

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPF1
• Ensembl ID: ENSOCUG00000014803
• Aliases: None
• Description: ribosome production factor 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:30350]

Sequence

>retro_ocun_1133
CAACAAACTTCTCCCAAGATTCTCATCACAACATCAGATAGACCTCATGGGAGAACAGTAAAACTTTGTGAACAGCTCTC
CACAGTTATACCAAACTCACATGTTTATTACAGAAGAGGACTGGCTCTGAAAAAAATTATTCCACAGTGCATTTCAAGAT
TTCACAGATCTGATTGTTATTAATGAAGATCGTAAAACACCAAATGGACTGATTCTGAGTCATTTGCCAAATGGTCCAAC
TGCTCATTTTAAAATGAGTAGTGTTCGTCTTCGTAAAGAAATTAAGAGAAGAGGCAAGGACCCCACAGAACACAGACCTG
AAATAATTCTGAATAATTTTACAACACGGCTAGGTCATTCTATTGGTCGTATGTTTGCTTCTCTCTTTCCCCATAATCCT
CAGTTTATTGGAAGGCAAGTTGCCACATTCCATAATCAGCAGGATTATATCTTCTTCAGATTTCACAGATACATATTCAA
GAGTGAAAAGAAAGCAGGAATTCAGGAACTTGGACCACGTTTTACCTTAAAATTAAGATCTCTTCAGAAAGGAACCTTTG
ATTCTAAATATGGAGAATATGAATGGGTCCATAAGCCCCGGGAAATGGACACAAGTAGAAGAAAATTTCATTTG

Alignment

ORF - retro_ocun_1133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.84 %
• Parental protein coverage: 60.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RQTSPKILITTSDRPHGRTVKLCEQLSTVIPNSHVYYRRGLAL-KKIIPQCISRDFTDLIVINEDRKTPN
          .QTSPKILITTSDRPHGRTVKLCEQLSTVIPNSHVYYRRGLAL.KK........DFTDLIVINEDRKTPN
Retrocopy QQTSPKILITTSDRPHGRTVKLCEQLSTVIPNSHVYYRRGLAL>KKLFHSAF-QDFTDLIVINEDRKTPN

Parental  GLILSHLPNGPTAHFKMSSVRLRKEIKRRGKDPTEHRPEIILNNFTTRLGHSIGRMFASLFPHNPQFIGR
          GLILSHLPNGPTAHFKMSSVRLRKEIKRRGKDPTEHRPEIILNNFTTRLGHSIGRMFASLFPHNPQFIGR
Retrocopy GLILSHLPNGPTAHFKMSSVRLRKEIKRRGKDPTEHRPEIILNNFTTRLGHSIGRMFASLFPHNPQFIGR

Parental  QVATFHNQRDYIFFRFHRYIFKSEKKAGIQELGPRFTLKLRSLQKGTFDSKYGEYEWVHKPREMDTSRRK
          QVATFHNQ.DYIFFRFHRYIFKSEKKAGIQELGPRFTLKLRSLQKGTFDSKYGEYEWVHKPREMDTSRRK
Retrocopy QVATFHNQQDYIFFRFHRYIFKSEKKAGIQELGPRFTLKLRSLQKGTFDSKYGEYEWVHKPREMDTSRRK

Parental  FHL
          FHL
Retrocopy FHL

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	12.91 RPM
SRP017611_kidney	0.00 RPM	16.22 RPM
SRP017611_liver	0.00 RPM	4.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1133 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1133 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1133 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001097	1 retrocopy	retro_eeur_17,
Myotis lucifugus	ENSMLUG00000016028	2 retrocopies	retro_mluc_681, retro_mluc_942,
Mus musculus	ENSMUSG00000028187	1 retrocopy	retro_mmus_3026,
Oryctolagus cuniculus	ENSOCUG00000014803	1 retrocopy	retro_ocun_1133 ,
Pteropus vampyrus	ENSPVAG00000003729	1 retrocopy	retro_pvam_1489,
Rattus norvegicus	ENSRNOG00000015969	1 retrocopy	retro_rnor_1372,
Tupaia belangeri	ENSTBEG00000013600	4 retrocopies	retro_tbel_1027, retro_tbel_2204, retro_tbel_2279, retro_tbel_63,