RetrogeneDB ID: retro_ocun_1828

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019131:143368..144478(+)
• 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_1828
ATGTTGTCATCTTGCTTACGCCTGGTTCCCATGACAGTCTGGTTTATGTAGTCTCTGAACTGCAATTCTTCCTGTTCCTT
CATGGGTCTGAAGACTCTCATTTCCTCCTTGAATGACTTTGCATCCCTGTCCTCTGCTGAGAGTTGGGACAATGTTGGAT
TGCTGGTGGAACCAAGCCCACCACAAACTATAAATACACTCTTCCTGACCAATGACTTGACTGAGCAGGTGATGGAGGAG
GCTCTGCATAAGAAGGCAGATCTCCTTCCACCTATCTTCCTACACATAAAGCATATTACCTGGATTTCCTGAAAGGAGCA
CCCGGTGTTCTGGGTTTTGGAGAACAGAGTTGGCATCTACTCTCTTCACACAGCCTATGATGCTGCACCCCAGGGATTGA
AAAACTGGTTTTCCAAAGGGCTTGGAGCCTGCACATCCAGGCATATATATCCTTCCAAAGCTCATGGCTATCCTATAGAG
GGAACCACTGAGAACAATTCAACATTAAGCATACCCAAGATATGGACAAAGTTGTGTCTGCAGTGAGAGAAGTTGAAGGT
GCTCCTGTCACTTCTTTTTCTGCTAGGATTGATGAGGAGAAAAACAAGGATCAGCCTGAATTGTACTGAGAAGTCTTTGA
TACAGGTGGTGGCTCAGCTCTCTCAAAACAGATAACTTTACCAGAGAACTGAAATTGTGTCCCTGCAGAAGCCTTTGCTC
TACATACTGGAATAGGTCGATCATGCACCCTGGATGAATCTGTTGCCCTGGCAACCATGATTGAGCAAATCAAAAGACAC
CTCAAACTAACTCGTATTAGCTCTTGGGGTAGGAAGGACCTTAGCATCATAAGTCAAAGCTGTGGCCCTGTGTGCTGGTT
CTGGGAGCAGCATCCTGCAGGATGTGGAAGCAGACCTGTACCTCACGGGTGGGATGTCCCATTATGATGGTCTGGATGCT
ACTTCCTAAGGAATAAATGCCATCCTCTGTGAACACAGTAACACTGAATGAGGCTTTCTTTCTGACCTTTGTGATAGTTT
GGGTGCCCACTTGGAGAATAAGATTAATATTATCTTGTCAGAGACAGACAGGGATCTTCTTTGTGTGATA

Alignment

ORF - retro_ocun_1828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLSSCARLAPSTVRLVHSLDCSSSRSFMDLKALISSLNDFASLSFAESWDNVGLLVEPSPPHTVNTLFLT
          MLSSC.RL.P.TV....SL.C.SS.SFM.LK.LISSLNDFASLS.AESWDNVGLLVEPSPP.T.NTLFLT
Retrocopy MLSSCLRLVPMTVWFM*SLNCNSSCSFMGLKTLISSLNDFASLSSAESWDNVGLLVEPSPPQTINTLFLT

Parental  NDLTEPVMEEALQKKADLILSYHPPIFLPMKRITWKSWKERLVIRALENRVAIYSPHTAYDAAPQGVNNW
          NDLTE.VMEEAL.KKADL.....PPIFL..K.ITW.S.KE..V...LENRV.IYS.HTAYDAAPQG..NW
Retrocopy NDLTEQVMEEALHKKADLL----PPIFLHIKHITWIS*KEHPVFWVLENRVGIYSLHTAYDAAPQGLKNW

Parental  LSKGLGACTSRPICPSKAHSYPTEGT-HRVEFNVNHTQDLDKVVSAVREIEGVSVTSFSARTDGEEQTR-
          .SKGLGACTSR.I.PSKAH.YP.EGT.H...FN..HTQD.DKVVSAVRE.EG..VTSFSAR.D.EE....
Retrocopy FSKGLGACTSRHIYPSKAHGYPIEGT<H*EQFNIKHTQDMDKVVSAVREVEGAPVTSFSARID-EEKNK>

Parental  ISLNCTEKALMQVVAQLSQNRQLYQRTEILSLEKPLL-LHTGMGRLCTLDESVSLATMIERIKRHLKLTH
          ISLNCTEK.L.QVVAQLSQNR.LYQRTEI.SL.KPLL.LHTG.GR.CTLDESV.LATMIE.IKRHLKLT.
Retrocopy ISLNCTEKSLIQVVAQLSQNR*LYQRTEIVSLQKPLL<LHTGIGRSCTLDESVALATMIEQIKRHLKLTR

Parental  I-RLALGVERTLESRVEVVALCAGSGSSVLRGVEADLYLTGEMSHHDVLDATSRGISVILCEHSNTERGF
          I..L..G..RTL.S.V..VALCAGSGSS.L..VEADLYLTG.MSH.D.LDATS.GI..ILCEHSNTE.GF
Retrocopy I>ALGVG--RTLAS*VKAVALCAGSGSSILQDVEADLYLTGGMSHYDGLDATS*GINAILCEHSNTE*GF

Parental  LSDLRDMLGVHLENRIHIVLSETDRDPLCVV
          LSDL.D.LG.HLEN.I.I.LSETDRD.LCV.
Retrocopy LSDLCDSLGAHLENKINIILSETDRDLLCVI

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_1828 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1828 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1828 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,