RetrogeneDB ID: retro_rnor_2408

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:1687130..1687906(+)
• 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_2408
CTGGGACTCTCCATGGGCTGCTGCTGGCACTGGTGCTGGCGTTCAGGGCCAAGAGCATGATGAGCAAGGAGCACATAGTT
TGTCCCGATTCAGATCTGGGCCTGTGGCCACCAGAGGACAAGCATAGCTTCCTGTATGATCATGAGGTCTTCCTGGGCAA
GGAGGACTCCAAGACCTTTGATAGCTAAGCCTGGATGAGAGCAAGGAGAGGCTGGGGAAAATTGTTGATCCAATAGACAG
TGATGGAGGCGGCCTTGTTACTACTGAGCAGCTGAAAATTTGGATCAAACAGGTACCAAAAAGATACATCTACCATAATG
TGGCTAAACTCTGGAAGGATTATGATAGGGACATAGACGAAAAGATCTCTTGGGAAGAATACAAGCAGTCCACTTATGGC
TACTACCTGGGAAACCTTGCTGAATTCCAAGATAGCTCTGATCATCACACCTTTAAAAAAATGCCTCCATGAGATGAGAG
GAGGTTTAAGGCTTCAGACATTGACAGCAACCTGACAGGTACTCGGGAGGGATTCATTGCCTTTCTGAACCCAGAGCAGT
TGAAACATATGAAGGAGATTGTAGTTCTGGAAACCCTGGAGGATATCGACAAGAACAGGGAAGGACTTGTGGACCAGGAT
GAGTATATTGTGGACATGTTTTTCCCATGAGGACAATGGCCCTGAGCCAGACTGGGTTTTGTCCAAATGGGAGCAGTTCA
ATGATTTCCCAGATCTGAACAAGGATGGGAAGCTGGACAAGGATGAGATTCGCCAC

Alignment

ORF - retro_rnor_2408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.15 %
• Parental protein coverage: 79.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LGLALG-LLLALVLALRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSKTFDQ-LSPDES
          LGL..G.LLLALVLA.RAK....KE..V.PDS.LG..PPED..SF.YDHE.FLGKEDSKTFD..LS.DES
Retrocopy LGLSMG<LLLALVLAFRAKSMMSKEHIVCPDSDLGLWPPEDKHSFLYDHEVFLGKEDSKTFDS<LSLDES

Parental  KERLGKIVDRIDSDGDGLVTTEELKVWIKRVQKRYIYDNVAKVWKDYDRDKDEKISWEEYKQATYGYYLG
          KERLGKIVD.IDSDG.GLVTTE.LK.WIK.V.KRYIY.NVAK.WKDYDRD.DEKISWEEYKQ.TYGYYLG
Retrocopy KERLGKIVDPIDSDGGGLVTTEQLKIWIKQVPKRYIYHNVAKLWKDYDRDIDEKISWEEYKQSTYGYYLG

Parental  NPAEFQDSSDHHTFKKMLPRDERRFKASDLDGDLTATREEFTAFLHPEEFEHMKEIVVLETLEDIDKNGD
          N.AEFQDSSDHHTFKKM.P.DERRFKASD.D..LT.TRE.F.AFL.PE...HMKEIVVLETLEDIDKN..
Retrocopy NLAEFQDSSDHHTFKKMPP*DERRFKASDIDSNLTGTREGFIAFLNPEQLKHMKEIVVLETLEDIDKNRE

Parental  GFVDQDEYIADM-FSHEDNGPEPDWVLSEREQFNDFRDLNKDGKLDKDEIRH
          G.VDQDEYI.DM.FSHEDNGPEPDWVLS..EQFNDF.DLNKDGKLDKDEIRH
Retrocopy GLVDQDEYIVDM>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_2408 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2408 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2408 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,