RetrogeneDB ID: retro_rnor_1224

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:38832362..38833261(-)
• 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_1224
CAGCTTGGGACTCTCCATGGACTGCTTCTGGCACTGGTGCTGGTGTTCAGGACCAAGAGCATGATGAGCAAGGAGCACAT
GGTTTGTCCCGATTCAGAGCTGGGCGAGTGGCCACCAGAAGACAAGCATAGCTTCCTGTACGATCATGAGGTCTTCTTGG
GCAAGGAGGACTTCAAGACCTTTGATAGCTAAGCGTGGATGAGAACAAGGAGAGGCTGGGGAAATTGTTGATCCAATTGA
CAGTGATGGAGGCGGCCTTGTTACTACTGAGCAGCTGGAAGTTTGGATCAAACAGGTACAGAAAAGATATATCTACTGTG
GCTAAACTCTGGAAGAATTATGATAGGGGCATAGACGAAAAGATCTCCTGGGAAGAATACAAGCAGTCCACTTATGGCTA
CTACCTGGGAAACCTTGCTGAATTCCAAGATAGCTCTAATCATCACACCTTTAAAAAGATGCCTCCATGAGATGAGAGGA
GGTTTAAGGTTTCAGACCTTGACAGCGACCTGACAGCTACTCAGGAGGGGTTCATTGCTTTTCTGCACCCAGAGGAGTTG
AAACATATGAAGGAGATTGTAGTTCTGGAAACCCTGGAGGATATCAACAAGAACGGGGATGGTTTGTGGACCAGGATGAG
TATATTGTGGACAAGTTTTTCCCACGAGGACAATGGCTCTGAGCCAGACCGTGTTTTGTCCAAATGGGAGCAGTTCAATG
ATTTCCTAGATCTGAACAAGGATGGGAAGCTGGATAAGGATGAGATTCGCCACTCGATCCTCCCTCAGGACTATGACCAT
GCAGGGGCTGAGGCCCGGTGTCTGGTATATGAGTCAGACAAAAACAAGGATGAGATGCTAACCAAGGAGGAGATTCTACA
AAACTGGAACATGTTTGTG

Alignment

ORF - retro_rnor_1224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.79 %
• Parental protein coverage: 92.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RLGLALGLLLALVLALRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSKTFDQ-LSPDES
          .LG...GLLLALVL..R.K....KE..V.PDSELGE.PPED..SF.YDHE.FLGKED.KTFD..LS.DE.
Retrocopy QLGTLHGLLLALVLVFRTKSMMSKEHMVCPDSELGEWPPEDKHSFLYDHEVFLGKEDFKTFDS<LSVDEN

Parental  KERLGKIVDRIDSDGDGLVTTEELKVWIKRVQKRYIYDNVAKVWKDYDRDKDEKISWEEYKQATYGYYLG
          KERLGK...........L......K....R..K......VAK.WK.YDR..DEKISWEEYKQ.TYGYYLG
Retrocopy KERLGKLLIQLTVMEAALLLLSSWKFGSNRYRKDI--STVAKLWKNYDRGIDEKISWEEYKQSTYGYYLG

Parental  NPAEFQDSSDHHTFKKMLPRDERRFKASDLDGDLTATREEFTAFLHPEEFEHMKEIVVLETLEDIDKNGD
          N.AEFQDSS.HHTFKKM.P.DERRFK.SDLD.DLTAT.E.F.AFLHPEE..HMKEIVVLETLEDI.KNGD
Retrocopy NLAEFQDSSNHHTFKKMPP*DERRFKVSDLDSDLTATQEGFIAFLHPEELKHMKEIVVLETLEDINKNGD

Parental  G-FVDQDEYIADMF-SHEDNGPEPDWVLSEREQFNDFRDLNKDGKLDKDEIRHWILPQDYDHAQAEARHL
          G.FVDQDEYI.D.F.SHEDNG.EPD.VLS..EQFNDF.DLNKDGKLDKDEIRH.ILPQDYDHA.AEAR.L
Retrocopy G<FVDQDEYIVDKF>SHEDNGSEPDRVLSKWEQFNDFLDLNKDGKLDKDEIRHSILPQDYDHAGAEARCL

Parental  VYESDKNKDEMLTKEEILDNWNMFV
          VYESDKNKDEMLTKEEIL.NWNMFV
Retrocopy VYESDKNKDEMLTKEEILQNWNMFV

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_1224 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1224 has 0 orthologous retrocopies within eutheria group .

---

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,