RetrogeneDB ID: retro_ocun_281

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:36898339..36899982(+)
• Located in intron of: ENSOCUG00000002551

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSBPL9
• Ensembl ID: ENSOCUG00000004303
• Aliases: None
• Description: oxysterol binding protein-like 9 [Source:HGNC Symbol;Acc:16386]

Sequence

>retro_ocun_281
CATTGTGTTGCTGCAGAAAGTACTATTAATCCTGTAGATGCAATATATCAGCCTAGTCCCTTGGAACCAGTGATCAGCAC
AATGCCTTCCCGGACTGTCTTACCTCCAGAACCTGCATAGTTGTGTAAGTCAAGCAGTGTCCACCTTCCCTACCAGTTGG
ACCTGTATTAGCTACTTTGGGACATCATCAGACTCCAACACCAAACAGTACAGGCAGTGGGCATTCACCACCTAGTAGCA
GTCTTACTTCTCCAAGCCATGTCAACTTGTCTCCAAATACAGTCCCAGAGTTCTCTTATTCTAGCAGTGAAAATGAATAC
TATGATGCTGATGAATTCCACCAAAGTGGCTCATCCCCAAAGCGCTTAATAGATTCTTCTGGATCTGCCTCTGTCTTGAC
ACACAGCAGCTCAGGAAATAGTATGAAGCGTCCAGATACCACAGAATCACTTAATTCCTCCATGTCTAATGGAACAAGTG
ATGTGGACCTTTTTGATTCGCATGACTATAGAGATGATGACGGAGAGGCAGGGTCAGTGGAGGAGCACAAGAGTGTTATC
ATGCACCTCTTGTCACAGGTTAGGCCCAGAATGGATCTAACTAAGGTAGTTCTTCCAACATTCATTCTTGAAAGAAGATC
TCTTTTAGAAATGTATGCAGACTTTTTTGCACATCCGGACCTATTTGTGAGCATTAGTGACCAGAAGGATCCTAGAGAGC
GAATGGTTCAGGTTGTGAAATGGTACCTCTCAGCCTTTCACACAGGAAGGAAAGAATCAGTTGCCAAAAAGCCATACAAC
CCCATTCTGGGTGAGATCTTTCAGTGTCACTGGACACTACCAAATGATACTGAAGAAAATGCAGAGCTAGTTTCTGAAGG
ACCAGTTCCCTGGGTTTCCAAAAACAGTGTAATGTTCGTGGCTGAACAGGTTTCCCATCATCCACCCATTTCAGCCTTTT
ATGCTGAGTGTTTTAACAAGAAGATCCAATTCAATTCTAATATCTGGACCAAATCAAAATTCCTTAGGATGTCGATTGGT
GTGCACAACATAGGGCAGGGCTGTGTTTCGTGTCTAGACTATGATGAACATTACATTCTCACATTTCCCAATGGTTATGG
AAGGTCTATCCTCATGGTGCCCTGGGTGGAATTGGGAGGAGAATGAAACATTAATTGTTCCAAAACGGGCTACAGTGCAA
ATATTGTCTTCCACACTAAACCTTTCTATAGGGGCAAGAAACACAGAATCGCTGCAGAGATTTTTTCTCCAAATGACAAG
AAGTCTTTTTGTTCCATTGAAGGAGAGTGGAATGGTGTAATGTATGCCAAATATGCAATGGGGGGAAACACAGTCTTTGT
AGATAACAAGAAGTTGCCTATAATCAAGAAGAAAATAAGGAAGTTGGAAGATCAGAATGAGTATGAGTCTCACTATCTTT
GGAAGGATGTCACTTTCAATCTAAAAATCAGAGACATCGATGCAGCCACTGAAGCAAAGCACAGACTTGAAGAAAGACAA
AGAGCAGAAGCCCGAGAAAGAAAGGAGAAGGAAATTCAGTGGGAGACAAGGTTATTTCATGAAGATGGAGAACGTTGGGT
TTATGATGAACCATTACTGAAACGTCTTGGTGCTGTCAAGCAT

Alignment

ORF - retro_ocun_281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.44 %
• Parental protein coverage: 74.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HADGIISTINPVDAIYQPSPLEPVISTMPSQTVLPPEPAQLCKS-EQRPSSLPVGPVLATLGHHQTPTPN
          H.....STINPVDAIYQPSPLEPVISTMPS.TVLPPEPA.LCKS..Q.P.SLPVGPVLATLGHHQTPTPN
Retrocopy HCVAAESTINPVDAIYQPSPLEPVISTMPSRTVLPPEPA*LCKS<KQCPPSLPVGPVLATLGHHQTPTPN

Parental  STGSGHSPPSSSLTSPSHVNLSPNTVPEFSYSSSEDEFYDADEFHQSGSSPKRLIDSSGSASVLTHSSSG
          STGSGHSPPSSSLTSPSHVNLSPNTVPEFSYSSSE.E.YDADEFHQSGSSPKRLIDSSGSASVLTHSSSG
Retrocopy STGSGHSPPSSSLTSPSHVNLSPNTVPEFSYSSSENEYYDADEFHQSGSSPKRLIDSSGSASVLTHSSSG

Parental  NSMKRPDTTESLNSSMSNGTSDADLFDSHDDRDDDGEAGSVEEHKSVIMHLLSQVRLGMDLTKVVLPTFI
          NSMKRPDTTESLNSSMSNGTSD.DLFDSHD.RDDDGEAGSVEEHKSVIMHLLSQVR..MDLTKVVLPTFI
Retrocopy NSMKRPDTTESLNSSMSNGTSDVDLFDSHDYRDDDGEAGSVEEHKSVIMHLLSQVRPRMDLTKVVLPTFI

Parental  LERRSLLEMYADFFAHPDLFVSISDQKEPRERMVQVVKWYLSAFHAGRKGSVAKKPYNPILGEIFQCHWT
          LERRSLLEMYADFFAHPDLFVSISDQK.PRERMVQVVKWYLSAFH.GRK.SVAKKPYNPILGEIFQCHWT
Retrocopy LERRSLLEMYADFFAHPDLFVSISDQKDPRERMVQVVKWYLSAFHTGRKESVAKKPYNPILGEIFQCHWT

Parental  LPNDTEENAELVSEGPVPWVSKNSVTFVAEQVSHHPPISAFYAECFNKKIQFNAHIWTKSKFLGMSIGVH
          LPNDTEENAELVSEGPVPWVSKNSV.FVAEQVSHHPPISAFYAECFNKKIQFN..IWTKSKFL.MSIGVH
Retrocopy LPNDTEENAELVSEGPVPWVSKNSVMFVAEQVSHHPPISAFYAECFNKKIQFNSNIWTKSKFLRMSIGVH

Parental  NIGQGCVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSKTGYSANIVFHTKPFYGGKKHRITA
          NIGQGCVSCLDYDEHYILTFPNGYGRSIL.VPWVELGGE.NINCSKTGYSANIVFHTKPFY.GKKHRI.A
Retrocopy NIGQGCVSCLDYDEHYILTFPNGYGRSILMVPWVELGGE*NINCSKTGYSANIVFHTKPFYRGKKHRIAA

Parental  EIFSPNDKKSFCSIEGEWNGVMYAKYATGENTVFVDTKKLPIIKKKVRKLEDQNEYESRCLWKDVTFNLK
          EIFSPNDKKSFCSIEGEWNGVMYAKYA.G.NTVFVD.KKLPIIKKK.RKLEDQNEYES..LWKDVTFNLK
Retrocopy EIFSPNDKKSFCSIEGEWNGVMYAKYAMGGNTVFVDNKKLPIIKKKIRKLEDQNEYESHYLWKDVTFNLK

Parental  IRDIDAATEAKHRLEERQRAEARERKEKEIQWETRLFHEDGECWVYDEPLLKRLGAAKH
          IRDIDAATEAKHRLEERQRAEARERKEKEIQWETRLFHEDGE.WVYDEPLLKRLGA.KH
Retrocopy IRDIDAATEAKHRLEERQRAEARERKEKEIQWETRLFHEDGERWVYDEPLLKRLGAVKH

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	0.17 RPM	45.64 RPM
SRP017611_kidney	0.20 RPM	164.70 RPM
SRP017611_liver	0.85 RPM	61.04 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_281 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_281 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021574	1 retrocopy	retro_cjac_1235,
Felis catus	ENSFCAG00000010298	1 retrocopy	retro_fcat_1134,
Gorilla gorilla	ENSGGOG00000004787	1 retrocopy	retro_ggor_737,
Microcebus murinus	ENSMICG00000002731	1 retrocopy	retro_mmur_1035,
Myotis lucifugus	ENSMLUG00000009199	1 retrocopy	retro_mluc_2149,
Nomascus leucogenys	ENSNLEG00000016138	2 retrocopies	retro_nleu_1820, retro_nleu_279,
Oryctolagus cuniculus	ENSOCUG00000004303	1 retrocopy	retro_ocun_281 ,
Pongo abelii	ENSPPYG00000001358	2 retrocopies	retro_pabe_689, retro_pabe_787,
Pan troglodytes	ENSPTRG00000000730	1 retrocopy	retro_ptro_632,
Ictidomys tridecemlineatus	ENSSTOG00000000692	1 retrocopy	retro_itri_1537,