RetrogeneDB ID: retro_ocun_1713

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018800:34486..35363(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021722
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUS1
• Ensembl ID: ENSOCUG00000011553
• Aliases: None
• Description: nuclear undecaprenyl pyrophosphate synthase 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21042]

Sequence

>retro_ocun_1713
ATGACGGGGCTGTACGAACTGGTGCGGCGGGTGCTGCACGCGCAGCTCTGCCTGCACCGCACGCTCACCTCCGCGTTCGC
GTTCGGTTCGGCACCTAGAACTGGATCTGGCGGCGCTGCTGTCGCGCCGCCTCCGCTGCGGTCCTAGCGCCGCTCGGCTT
CACGCTCCGCAAGCCTCGGGCCTTGGCAGGAACCACCGGCACTACCGGCACCCGCGCTGGGGCCGGGTCTGGCCTCCGCC
CACCCCCGGCTGCGCTGGCGCGCGGACGGCAGTTCCCTGGACAAGCTGCCTGTGCACTTGGGCTTCGTGATCACCGAGGA
GGAGCCGGAGCCCAGCTTCTCGGACATCGCGAGCCTCGTAGTGTGGTGTATGGCCGTGGGCATCTCCTACATTAGCGTCT
ACGACCACCAAGGTATTTTCAAAAGAAACAAGTCCAGACTGATGGATGAAATTTTAAAACAGCAACAGGAACTTCTGGGC
CTGGATTGTTCCAAATACTCAACAGGGTTTGCAAATAGTAATGACAAAGATGATCAAGTTTTAAATTGCCATTCAGCAGT
GCAGGTGCTGTCCCCAGAAGGTGGAAAAGCAGATATTGTGAGAGCTGCTCAGGACTTTTGCCAGTTAGTAGCCCAGCAGC
AGAAGAAATCCACAGATTTGCATGTAGATATGTTAGACAGTTTACTTAGTTCAAATGGTTTCCCTGATCCTGATTTAGTA
TTGAAGTTTGGTCCTGTGGACAGCACATTAGGCTTTCTTCCCCTGGCACATCAGATGGACTGAGATTGTCTCTTTGCCTT
CCCACCTAAACATCAGTTATGAGGACTTTTTCTCTGCCCTTCGTCAATATGCAGCCTGCGAACAACGTCTGGGAAAG

Alignment

ORF - retro_ocun_1713 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MTGLYELVWRVLHALLCLHRTLTSW-LRVRFGTWNWIWRRCCRAASAAVLAPLGFTLRKPPAV-GRNRRH
          MTGLYELV.RVLHA.LCLHRTLTS...RVRFGT.NWIWRRCCRAASAAVLAPLGFTLRKP.A..GRN.RH
Retrocopy MTGLYELVRRVLHAQLCLHRTLTSA<VRVRFGT*NWIWRRCCRAASAAVLAPLGFTLRKPRAL<GRNHRH

Parental  YRHPRGG-PGLASAHPRLRWRADGRSLDKLPVHMGLVITEEEQEPSFSDIASLVVWCMAVGISYISVYDH
          YRHPR.G.PGLASAHPRLRWRADG.SLDKLPVH.G.VITEEE.EPSFSDIASLVVWCMAVGISYISVYDH
Retrocopy YRHPRWG<PGLASAHPRLRWRADGSSLDKLPVHLGFVITEEEPEPSFSDIASLVVWCMAVGISYISVYDH

Parental  QGIFKRNNSRLMDEILKQQQELLGLDCSKYSTEFANSNDKDDQVLNCHSAVKVLSPEDGKADIVRAAQDF
          QGIFKRN.SRLMDEILKQQQELLGLDCSKYST.FANSNDKDDQVLNCHSAV.VLSPE.GKADIVRAAQDF
Retrocopy QGIFKRNKSRLMDEILKQQQELLGLDCSKYSTGFANSNDKDDQVLNCHSAVQVLSPEGGKADIVRAAQDF

Parental  CQLVAQQQKKSTDLDVDMLDSLLSSNGFPDPDLVLKFGPMDSTLGFL-PWHIRLTEIVSLPSHLNISYED
          CQLVAQQQKKSTDL.VDMLDSLLSSNGFPDPDLVLKFGP.DSTLGFL.PWHIR.TEIVSLPSHLNISYED
Retrocopy CQLVAQQQKKSTDLHVDMLDSLLSSNGFPDPDLVLKFGPVDSTLGFL>PWHIRWTEIVSLPSHLNISYED

Parental  FFSALRQYAACEQRLGK
          FFSALRQYAACEQRLGK
Retrocopy FFSALRQYAACEQRLGK

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	0.28 RPM	11.20 RPM
SRP017611_kidney	1.62 RPM	12.06 RPM
SRP017611_liver	0.31 RPM	6.71 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1713 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1713 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1713 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001780	1 retrocopy	retro_dnov_1639,
Erinaceus europaeus	ENSEEUG00000008948	1 retrocopy	retro_eeur_443,
Homo sapiens	ENSG00000153989	4 retrocopies	retro_hsap_1174, retro_hsap_1176, retro_hsap_1289, retro_hsap_4825,
Gorilla gorilla	ENSGGOG00000022321	4 retrocopies	retro_ggor_1012, retro_ggor_914, retro_ggor_915, retro_ggor_993,
Microcebus murinus	ENSMICG00000007831	1 retrocopy	retro_mmur_423,
Nomascus leucogenys	ENSNLEG00000013457	1 retrocopy	retro_nleu_2411,
Oryctolagus cuniculus	ENSOCUG00000011553	1 retrocopy	retro_ocun_1713 ,
Pongo abelii	ENSPPYG00000025886	1 retrocopy	retro_pabe_81,
Pan troglodytes	ENSPTRG00000018547	1 retrocopy	retro_ptro_808,
Tarsius syrichta	ENSTSYG00000003212	1 retrocopy	retro_tsyr_633,
Tursiops truncatus	ENSTTRG00000007352	2 retrocopies	retro_ttru_358, retro_ttru_684,