RetrogeneDB ID: retro_rnor_899

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:3473374..3473700(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Exosc1
• Ensembl ID: ENSRNOG00000048708
• Aliases: None
• Description: exosome component 1 [Source:MGI Symbol;Acc:MGI:1913833]

Sequence

>retro_rnor_899
GTGAGATACTGCATACCTGAAAAACATCGGTGTAACTAGGAGGAAGGTAGTCTGAGTAGTGGCACCTGTATCAGGCATAG
CTATATCTTTTTGTTGTTGTTGACATTTCCAACAAAAAACAATAACAATGGTGTTGTTTCTGTGATTTGTGTGATGACAA
AAACGGAAACCCAAATATTTCCAGAAATGACAGCTTTTGTCCCTTGTAAGGTCTTTAGCCTCAATTTATATTTTGCCAAA
GTAGACATCCTATATGTGGGATCCACAACACTAAAAATAATTTTTGTGGAACTACCTGCAAGAAAAAAATCCAAGCAACT
GTAAAA

Alignment

ORF - retro_rnor_899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.45 %
• Parental protein coverage: 55.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRYCIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLTKTSENGALPVVSVMRETESQLLPDVGAVVTCK
          VRYCIP....CN.EEGS..SGT..RH.YIF..L....TK...NG...V..VM..TE.Q..P...A.V.CK
Retrocopy VRYCIPEKHRCN*EEGSLSSGTCIRHSYIFLLLLTFPTKNNNNGVVSVICVMTKTETQIFPEMTAFVPCK

Parental  VSSINSRFAKVHILYVGSTPL-KNAFRGTIRKEDIRATEK
          V.S.N..FAKV.ILYVGST.L.KN.F.GT..K..I.AT.K
Retrocopy VFSLNLYFAKVDILYVGSTTL<KNNFCGTTCKKKIQATVK

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	7.55 RPM
SRP017611_kidney	0.00 RPM	4.47 RPM
SRP017611_liver	0.00 RPM	4.37 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_899 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_899 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_899 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006477	1 retrocopy	retro_chof_2075,
Dasypus novemcinctus	ENSDNOG00000007983	1 retrocopy	retro_dnov_104,
Erinaceus europaeus	ENSEEUG00000005647	3 retrocopies	retro_eeur_270, retro_eeur_438, retro_eeur_464,
Macropus eugenii	ENSMEUG00000002246	2 retrocopies	retro_meug_1799, retro_meug_951,
Myotis lucifugus	ENSMLUG00000009228	1 retrocopy	retro_mluc_1563,
Mus musculus	ENSMUSG00000034321	1 retrocopy	retro_mmus_691,
Oryctolagus cuniculus	ENSOCUG00000011898	1 retrocopy	retro_ocun_173,
Otolemur garnettii	ENSOGAG00000016259	1 retrocopy	retro_ogar_2496,
Pteropus vampyrus	ENSPVAG00000003372	1 retrocopy	retro_pvam_686,
Rattus norvegicus	ENSRNOG00000048708	1 retrocopy	retro_rnor_899 ,
Ictidomys tridecemlineatus	ENSSTOG00000006615	1 retrocopy	retro_itri_1253,