RetrogeneDB ID: retro_rnor_1090

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:17709963..17710481(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl10
• Ensembl ID: ENSRNOG00000027149
• Aliases: None
• Description: 60S ribosomal protein L10 [Source:UniProtKB/Swiss-Prot;Acc:Q6PDV7]

Sequence

>retro_rnor_1090
CTGCATCTTTTTGACTTGGGCCGGAAGAAGGCAAAAGTTGATGAATTCCTACTTTGTGGCCACATGGTGTCAGATGAATA
CGTACAGCTTTCTTCTGAAACCCTGGAAGCTGACTGTATATCTGCCAACAAATATGCGGTAAAGAGTTGTGACAATGCTG
GCTTTTGTATCTGAGTAGGACTCCACCCTTTTCATATCATTCGCAACAACAAAGATGCTGTCCTGTACCGGGGTTGACAG
ACTCCAGCCAGGTATACAGGGACTTTGCGAAGCCCCAGGGCACAGTGGCCAGGGTTCCCATTGGCCACATATGGTGATGT
CCATCTGCACCAGGCTGCGGAATAAGGAGCATGTGATTGAGGCTCTGCATAGAGCACAAGTACAAGTTCCCTGGCCTACG
GAAGATCCACATCTCAAAGGAGTGGGACTTCACCAAATTTAAAGCAGATGAGTTTGAAGACATGGTTAATGAGAAGTGGC
TCATTCCTGATGGCTCTGGGGTCAGACACATCCCCAGT

Alignment

ORF - retro_rnor_1090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.24 %
• Parental protein coverage: 80.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRIN
          ...FDLGRKKAKVDEF.LCGHMVSDEY.QLSSE.LEA..I.ANKY.VKSC...GF.I.V.LHPFH.IR.N
Retrocopy LHLFDLGRKKAKVDEFLLCGHMVSDEYVQLSSETLEADCISANKYAVKSCDNAGFCI*VGLHPFHIIRNN

Parental  -KMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRA-KFKFPGRQKIHIS
          .KMLSC.G.DRLQ.G..G....P.......H.....MSI.T.L.NKEHVIEAL.RA.K.KFPG..KIHIS
Retrocopy >KMLSCTGVDRLQPGIQGLCEAPGHSGQGSHWPHMVMSICTRLRNKEHVIEALHRA>KYKFPGLRKIHIS

Parental  KKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPN
          K.W.FTKF.ADEFEDMV.EK.LIPDG.GV..IP.
Retrocopy KEWDFTKFKADEFEDMVNEKWLIPDGSGVRHIPS

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	114.60 RPM
SRP017611_kidney	0.00 RPM	230.91 RPM
SRP017611_liver	0.00 RPM	218.39 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1090 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1090 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1090 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011822	5 retrocopies	retro_cjac_156, retro_cjac_174, retro_cjac_260, retro_cjac_277, retro_cjac_61,
Felis catus	ENSFCAG00000011395	1 retrocopy	retro_fcat_81,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Oryctolagus cuniculus	ENSOCUG00000015919	2 retrocopies	retro_ocun_107, retro_ocun_147,
Rattus norvegicus	ENSRNOG00000027149	5 retrocopies	retro_rnor_1007, retro_rnor_1090 , retro_rnor_270, retro_rnor_2998, retro_rnor_482,