RetrogeneDB ID: retro_ocun_1334

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:149412261..149412719(+)
• Located in intron of: ENSOCUG00000010509

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYB
• Ensembl ID: ENSOCUG00000004415
• Aliases: None
• Description: nuclear transcription factor Y, beta [Source:HGNC Symbol;Acc:7805]

Sequence

>retro_ocun_1334
GTGACAATGTATGATGGCAGTTCCATCACAGATACTTCTCAACTGGAAATTCCAGGAGACTACGTTGGAGGTAGCAGCTA
TGTTATACAACCTCACAATGATGCTGAGGACAGCATGAGTGATCACGAAGACACAAATGGATCAAAAAAAAGTTTCCAAG
AACGAGATTATTTTCCACTGTGACAAAGGTAATGAAGAATGCCCTACCTCAAACAGGAAAGATTGCAAAAGATGCCTAAG
AATGTGTTCAAGGATGTGTGAGTGAGTTCATTAGCTTTGTACCATCTGAAGCAAATGAAAGTTGTCATCAATAGAAACAG
AAGACAATCAATGGAGAAGACATTCTCTTTGCCATGTCCACCTTGGACTTTGACCCTTATATGGAGCCTCCAAAACTGCA
CCTTTAGAAATTCAGAGAGGCTATGGAAAGAGAGAAAGGAATTGATGGAGCAGCCACA

Alignment

ORF - retro_ocun_1334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.15 %
• Parental protein coverage: 75.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTMDGDSSTTDASQLGISADYIGGSHYVIQPHDDTEDSMNDHEDTNGS-KESFREQDIYLPIANVARIMK
          .TM...SS.TD.SQL.I..DY.GGS.YVIQPH.D.EDSM.DHEDTNGS.K..F...........V...MK
Retrocopy VTMYDGSSITDTSQLEIPGDYVGGSSYVIQPHNDAEDSMSDHEDTNGS<KKKFPRTRLF---STVTKVMK

Parental  NAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQ
          NA.PQTGKIAKDA.ECVQ.CVSEFISF..SEA.E.CHQ.K.KTINGEDILFAMSTL.FD.Y.EP.KL.L.
Retrocopy NALPQTGKIAKDA*ECVQGCVSEFISFVPSEANESCHQ*KQKTINGEDILFAMSTLDFDPYMEPPKLHL*

Parental  KFREAMKGEKGIGGAVT
          KFREAM..EKGI.GA.T
Retrocopy KFREAMEREKGIDGAAT

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	33.00 RPM
SRP017611_kidney	0.00 RPM	13.78 RPM
SRP017611_liver	0.00 RPM	14.18 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1334 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1334 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1334 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006686	1 retrocopy	retro_amel_940,
Bos taurus	ENSBTAG00000030744	1 retrocopy	retro_btau_1681,
Canis familiaris	ENSCAFG00000029177	1 retrocopy	retro_cfam_1677,
Callithrix jacchus	ENSCJAG00000014610	1 retrocopy	retro_cjac_1133,
Cavia porcellus	ENSCPOG00000003213	1 retrocopy	retro_cpor_901,
Felis catus	ENSFCAG00000026471	1 retrocopy	retro_fcat_207,
Homo sapiens	ENSG00000120837	2 retrocopies	retro_hsap_2827, retro_hsap_4047,
Gorilla gorilla	ENSGGOG00000008866	1 retrocopy	retro_ggor_2714,
Myotis lucifugus	ENSMLUG00000005468	1 retrocopy	retro_mluc_1764,
Macaca mulatta	ENSMMUG00000022570	3 retrocopies	retro_mmul_1433, retro_mmul_2119, retro_mmul_2335,
Mustela putorius furo	ENSMPUG00000012064	3 retrocopies	retro_mputfur_1531, retro_mputfur_1563, retro_mputfur_1567,
Nomascus leucogenys	ENSNLEG00000006543	2 retrocopies	retro_nleu_1203, retro_nleu_2061,
Oryctolagus cuniculus	ENSOCUG00000004415	4 retrocopies	retro_ocun_1334 , retro_ocun_1816, retro_ocun_1824, retro_ocun_1845,
Ochotona princeps	ENSOPRG00000008117	2 retrocopies	retro_opri_36, retro_opri_657,
Ictidomys tridecemlineatus	ENSSTOG00000005279	1 retrocopy	retro_itri_1851,
Tupaia belangeri	ENSTBEG00000005731	1 retrocopy	retro_tbel_4360,