RetrogeneDB ID: retro_rnor_2409

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:1692237..1693022(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rcn1
• Ensembl ID: ENSRNOG00000013452
• Aliases: Rcn1, Rcn
• Description: reticulocalbin-1 precursor [Source:RefSeq peptide;Acc:NP_001102056]

Sequence

>retro_rnor_2409
GGTGTCAGCCTGGGACTCTCCATGGGCTGCTGCTGGCACTGGTGCTGGCGTTCAGGTCCAAGAGCATGATGAGCAAGGAG
CACATAGTTTGTCCCGATTCAGAGCTGGGCCAGTGGCCACCAGAGGACAAGCACACCTTCCTGTATGATCATGAGGTCTT
CCTGGGCAAGGAGCATTCCAAGACCTTTGATAGCTAAGCCTGGATGAGAGCAAGGAGAGGCTGGGGAAAATTGTTGATCC
AATAGACAGTGATGGAGGCGGCCTTGTTACTACTGAGCAGCTGAAAGTTTGGATCAAACAGGTACCAAAAAGATACATCT
ACCATAATGTGGCTAAACTCTGGAAGGATTATGATAGGGACATAGACGAAAAGATCTCCTGGGAAGAATACAAGCAGTCC
ACTTATGGCTACTACCTGGGAAACCTTGCTGAATTCCAAGATAGCTCTGATCATCACACCTTTAAAAAAATGCCTCCATG
AGATGAGAGGAGGTTTAAGGCTTCAGACATTGACAGCAACCTGACAGGTACTCGGGAGGGATTCATTGCCTTTCTGAACC
CAGAGCAGTTGAAACATATGAAGGAGATTGTAGTTCTGGAAACCCTGGAGGATATCGACAAGAACAGGGAAGGACTTGTG
GACCAGGATGAGTATATTGTGGATATGTTTTTCCCATGAGGACAATGGCCCTGAGCCAGACTGGGTTTTGTCCAAATGGG
AGCAGTTCAATGATTTCCCAGATCTGAACAAGGATGGGAAGCTGGACAAGGATGAGATTCGCCAC

Alignment

ORF - retro_rnor_2409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.25 %
• Parental protein coverage: 80.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGRLGLALG-LLLALVLALRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSKTFDQ-LSP
          G..LGL..G.LLLALVLA.R.K....KE..V.PDSELG..PPED...F.YDHE.FLGKE.SKTFD..LS.
Retrocopy GVSLGLSMG<LLLALVLAFRSKSMMSKEHIVCPDSELGQWPPEDKHTFLYDHEVFLGKEHSKTFDS<LSL

Parental  DESKERLGKIVDRIDSDGDGLVTTEELKVWIKRVQKRYIYDNVAKVWKDYDRDKDEKISWEEYKQATYGY
          DESKERLGKIVD.IDSDG.GLVTTE.LKVWIK.V.KRYIY.NVAK.WKDYDRD.DEKISWEEYKQ.TYGY
Retrocopy DESKERLGKIVDPIDSDGGGLVTTEQLKVWIKQVPKRYIYHNVAKLWKDYDRDIDEKISWEEYKQSTYGY

Parental  YLGNPAEFQDSSDHHTFKKMLPRDERRFKASDLDGDLTATREEFTAFLHPEEFEHMKEIVVLETLEDIDK
          YLGN.AEFQDSSDHHTFKKM.P.DERRFKASD.D..LT.TRE.F.AFL.PE...HMKEIVVLETLEDIDK
Retrocopy YLGNLAEFQDSSDHHTFKKMPP*DERRFKASDIDSNLTGTREGFIAFLNPEQLKHMKEIVVLETLEDIDK

Parental  NGDGFVDQDEYIADM-FSHEDNGPEPDWVLSEREQFNDFRDLNKDGKLDKDEIRH
          N..G.VDQDEYI.DM.FSHEDNGPEPDWVLS..EQFNDF.DLNKDGKLDKDEIRH
Retrocopy NREGLVDQDEYIVDM>FSHEDNGPEPDWVLSKWEQFNDFPDLNKDGKLDKDEIRH

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	46.66 RPM
SRP017611_kidney	0.00 RPM	28.40 RPM
SRP017611_liver	0.00 RPM	8.94 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2409 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2409 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2409 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000049449	2 retrocopies	retro_hsap_1259, retro_hsap_3629,
Pongo abelii	ENSPPYG00000003385	1 retrocopy	retro_pabe_2976,
Rattus norvegicus	ENSRNOG00000013452	28 retrocopies	retro_rnor_1207, retro_rnor_1224, retro_rnor_2111, retro_rnor_2112, retro_rnor_2113, retro_rnor_2352, retro_rnor_2353, retro_rnor_2354, retro_rnor_2355, retro_rnor_2408, retro_rnor_2409 , retro_rnor_2410, retro_rnor_2434, retro_rnor_2435, retro_rnor_2436, retro_rnor_2437, retro_rnor_2438, retro_rnor_2486, retro_rnor_2508, retro_rnor_2509, retro_rnor_2510, retro_rnor_2511, retro_rnor_2513, retro_rnor_2664, retro_rnor_2711, retro_rnor_2716, retro_rnor_2760, retro_rnor_797,