RetrogeneDB ID: retro_ocun_1558

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018700:6306870..6307484(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTPBP10
• Ensembl ID: ENSOCUG00000014847
• Aliases: None
• Description: GTP-binding protein 10 (putative) [Source:HGNC Symbol;Acc:25106]

Sequence

>retro_ocun_1558
AAAAATGGCAAAATTACAGAACTCAATAAAAAGGACAGAATTTTGGTGACTGAAGGAGGTCTTGATGATAAATTACTTAC
AAATTTCTTACCATTAAAGGGCAAAAATGAATAATTCACCTTGATCTAAAACTGTAGTTGATGTAGGACCAGCAGGGTTC
CCAAATGCTTGAAAATCCTCTTTACTAAGTTGAGTTTCTCATGCAATGCCCACTATTGAAGATCATGCATTTACGTTAAA
GTCAGAAGTTGGAAAGATTATATGTATTGATTTCAAACAAATATCTGTAGCTGATCTTCCTGGTTTGATAGAAGGAACAC
ATATGAACAAAAGAAAGGTCCACCATTTCTCAAGCATAGAGAGAGATATATATCTACTTATTGTTTTTGATATTTCTGGA
TTTCAGCTTTCATTCCAAACTCATTATGCAATTGCCTTTGAAACCATAATACTACTCACAAAAGATTTGGGATTCGTACA
AAGAGGAACTTCAGATAAAACCTGCACTCCTGGCAGTTAATAAAATGGACTTACCCAACGTTCAAGATAAATTCCATGAA
CTGATAAACCAACTCCAGAGTCCTAAAGATTTTTTGCTCTTATTTGAAAGAACA

Alignment

ORF - retro_ocun_1558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.17 %
• Parental protein coverage: 52.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ENGKIIGELNKEEDRILVAEGGLGGKLLTNFLPLKG-QKRIIHLDLKL-TADVGLVGFPNAGKSSLLSRV
          .NGKI..ELNK..DRILV.EGGL..KLLTNFLPLKG.QK.IIHLDLKL...DVG..GFPNA.KSSLLS.V
Retrocopy KNGKIT-ELNKK-DRILVTEGGLDDKLLTNFLPLKG<QK*IIHLDLKL<VVDVGPAGFPNA*KSSLLS*V

Parental  SHAKPAIADYAFTTLKPQLGKIMYSDYKQISVADLPGLIEGAHMNKGMGHKFLKHIERTRHLLFVVDISG
          SHA.P.I.D.AFT.LK...GKI...D.KQISVADLPGLIEG.HMNK...H.F...IER...LL.V.DISG
Retrocopy SHAMPTIEDHAFT-LKSEVGKIICIDFKQISVADLPGLIEGTHMNKRKVHHF-SSIERDIYLLIVFDISG

Parental  FQLSSQTHYRTAFETIILLTKEL-ELYKEELQTKPALLAVNKMDLPGARDKFQDLMNQLQNPKDFLHLFE
          FQLS.QTHY..AFETIILLTK.L...YKEELQ.KPALLAVNKMDLP...DKF..L.NQLQ.PKDFL.LFE
Retrocopy FQLSFQTHYAIAFETIILLTKDL>DSYKEELQIKPALLAVNKMDLPNVQDKFHELINQLQSPKDFLLLFE

Parental  RS
          R.
Retrocopy RT

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	5.74 RPM
SRP017611_kidney	0.00 RPM	7.09 RPM
SRP017611_liver	0.00 RPM	3.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1558 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1558 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014212	1 retrocopy	retro_cjac_563,
Myotis lucifugus	ENSMLUG00000007418	1 retrocopy	retro_mluc_789,
Mus musculus	ENSMUSG00000040464	1 retrocopy	retro_mmus_3183,
Oryctolagus cuniculus	ENSOCUG00000014847	1 retrocopy	retro_ocun_1558 ,
Otolemur garnettii	ENSOGAG00000010568	1 retrocopy	retro_ogar_431,
Sus scrofa	ENSSSCG00000015305	1 retrocopy	retro_sscr_661,