RetrogeneDB ID: retro_ocun_1534

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: AAGW02079181:602..1493(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000010667
• Aliases: None
• Description: None

Sequence

>retro_ocun_1534
CTGATGGAGGAGGCTCTGCATAAGAAGGCAGATCTCATCTTTTCCTGCCTTCCACCTATCTTCCTACACATAAAGCATAT
TACCTGGATGTCCTGAAAGGAGCGCCCAGTGTTCTGGGCTTTGGAGAACAGAGTTGGCATCTACTCTCTTCACACAGCCT
ATGATGCTGCACCCCAGGGATTGAAAAACTGGTTTTCCAAAGGGCTTGGAGCCTGCACATCCAGGCATATATATCCTTCC
AAAGCTCATGGCTATCCTATAGAGGGAACCACTGAGTGCAATTCAACATTAAGCATACCCAAGATATGGACAAAGTTGTG
TCTGCAGTGAAAGTTGAAGGTGCTCCTGTCACTTCTTTTTCTGCTAGGATTGATGAGGAGAAAAACAAGGATCAGCCTGA
ATTGTACTGAGAAGTCTTTGATACAGGTGGTGGCTCAGCTTTCTCAAAACAGATAACTTTACCAGAGAACTGAAATTGTG
TCACTGCAGAAGCCTTTGCTCTGCATACTGGAATAGGTCGATCATGCACCCTGGATGAATCTGTTGCCCTGGCAACCATG
ATTGAGTGAATCAAAAGACACCTCAAACTAACTCATATTAGCTCTTGGGGTAGGAAGGACCTTAGCATCATGAGTCAAAG
CTGTGGCCCTGTGTGCTGGTTCTGGGAGCAGCATCCTGCAGGATGTGGAAGCAGACCTGTACTTCACGGGTGGGATGTCC
CATTATGATGGTCTGGATGCTACTTCCTAAGGAATAAATGCCATCCTCTGTGAACACAGTAACACTGAATGAGGCTTTCT
TTCTGACCTTTGTGATATTCTGGGTGCCCACTTGGAGAACAAGATTAATATTATCTTGTCAGAGACAGACAGGGATCTTC
TTTGTGTGGTA

Alignment

ORF - retro_ocun_1534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.75 %
• Parental protein coverage: 79.84 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VMEEALQKKADLILSYHPPIFLPMKRITWKSWKERLVIRALENRVAIYSPHTAYDAAPQGVNNWLSKGLG
          .MEEAL.KKADLI.S..PPIFL..K.ITW.S.KER.V..ALENRV.IYS.HTAYDAAPQG..NW.SKGLG
Retrocopy LMEEALHKKADLIFSCLPPIFLHIKHITWMS*KERPVFWALENRVGIYSLHTAYDAAPQGLKNWFSKGLG

Parental  ACTSRPICPSKAHSYPTEGT-HRVEFNVNHTQDLDKVVSAVREIEGVSVTSFSARTDGEEQTR-ISLNCT
          ACTSR.I.PSKAH.YP.EGT.H.V.FN..HTQD.DKVVSAV...EG..VTSFSAR.D.EE....ISLNCT
Retrocopy ACTSRHIYPSKAHGYPIEGT<H*VQFNIKHTQDMDKVVSAVK-VEGAPVTSFSARID-EEKNK>ISLNCT

Parental  EKALMQVVAQLSQNRQLYQRTEILSLEKPLL-LHTGMGRLCTLDESVSLATMIERIKRHLKLTHI-RLAL
          EK.L.QVVAQLSQNR.LYQRTEI.SL.KPLL.LHTG.GR.CTLDESV.LATMIE.IKRHLKLTHI..L..
Retrocopy EKSLIQVVAQLSQNR*LYQRTEIVSLQKPLL<LHTGIGRSCTLDESVALATMIE*IKRHLKLTHI>ALGV

Parental  GVERTLESRVEVVALCAGSGSSVLRGVEADLYLTGEMSHHDVLDATSRGISVILCEHSNTERGFLSDLRD
          G..RTL.S.V..VALCAGSGSS.L..VEADLY.TG.MSH.D.LDATS.GI..ILCEHSNTE.GFLSDL.D
Retrocopy G--RTLAS*VKAVALCAGSGSSILQDVEADLYFTGGMSHYDGLDATS*GINAILCEHSNTE*GFLSDLCD

Parental  MLGVHLENRIHIVLSETDRDPLCVV
          .LG.HLEN.I.I.LSETDRD.LCVV
Retrocopy ILGAHLENKINIILSETDRDLLCVV

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	9.99 RPM
SRP017611_kidney	0.00 RPM	15.71 RPM
SRP017611_liver	0.00 RPM	5.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1534 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1534 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1534 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023186	1 retrocopy	retro_fcat_589,
Macaca mulatta	ENSMMUG00000006639	1 retrocopy	retro_mmul_444,
Nomascus leucogenys	ENSNLEG00000006935	1 retrocopy	retro_nleu_1504,
Oryctolagus cuniculus	ENSOCUG00000010667	16 retrocopies	retro_ocun_1105, retro_ocun_1534 , retro_ocun_1539, retro_ocun_1691, retro_ocun_1692, retro_ocun_1710, retro_ocun_1729, retro_ocun_1749, retro_ocun_1789, retro_ocun_1828, retro_ocun_1837, retro_ocun_1841, retro_ocun_1846, retro_ocun_1847, retro_ocun_1854, retro_ocun_929,
Pongo abelii	ENSPPYG00000013063	1 retrocopy	retro_pabe_244,
Tupaia belangeri	ENSTBEG00000000704	1 retrocopy	retro_tbel_3512,