RetrogeneDB ID: retro_rnor_2267

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:167986381..167987025(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Csnk1g1
• Ensembl ID: ENSRNOG00000016620
• Aliases: None
• Description: Casein kinase I isoform gamma-1 [Source:UniProtKB/Swiss-Prot;Acc:Q62761]

Sequence

>retro_rnor_2267
GAAAAAATTGGATGTGGCAATTTTAGAGAATTACGATTAGGGAAAAGTTTATATAAAAATGAATATGTGGCGATTAAACT
GGAGCCCATGAAATCTAGAGCACCACAGCTGCATTTGGAATGCAAATTCTATAAGCAGTTAGCATCTGGAGATGGTATAC
CTCAAGTTTACTGTTTTGGCCCATGTGGTAAATACAATGGTACGGTGCTTGAACTGCTGGGACCTAGTTTGGAAGATTTG
TTTGACCTCTGTGATAGAACATTTTCTCTTAAAAGAGTTCTCATGATAGCTATACAACCAATTTCTTGCATGGAGTATAT
CAACTCAAAGAACTTATATACAGACATATGAAGCCTGAGAATTTCTTAATAGGATGGTCAGGGAACAAAGCCCAGCAAGT
CACTCATATCATAGATTTTGGTTTGACAAAGGTTTGAATATATTGATCCAGAGACAAAGAAACATATACCATACAGAGAA
CACGAATCCTTACTGGAACAGCTAGATACATGAGCTTAAACACACATCTAGGAAAAGAACAGAGTAGAAGAGCTGATTTA
TTAGGAGCTTTAAGCCATATGTTCATGTACTTCTTGAGAGGTGGTCTTCCTTGGCACGCCTTAAAGGTCCATACATTAAG
AGAG

Alignment

ORF - retro_rnor_2267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.81 %
• Parental protein coverage: 54.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKIGCGNFGELRLGKNLYTNEYVAIKLEPIKSRAPQLHLEYRFYKQLGSAGEGLPQVYYFGPCGKYNAMV
          .KIGCGNF.ELRLGK.LY.NEYVAIKLEP.KSRAPQLHLE..FYKQL.S.G.G.PQVY.FGPCGKYN..V
Retrocopy EKIGCGNFRELRLGKSLYKNEYVAIKLEPMKSRAPQLHLECKFYKQLAS-GDGIPQVYCFGPCGKYNGTV

Parental  LELLGPSLEDLFDLCDRTFTLKTVLMIAIQLLSRMEYVHSKN-LIYRDVKPENFLIGRQGNKKEHVIHII
          LELLGPSLEDLFDLCDRTF.LK.VLMIAIQ..S.MEY..SKN.LIYR..KPENFLIG..GNK...V.HII
Retrocopy LELLGPSLEDLFDLCDRTFSLKRVLMIAIQPISCMEYINSKN<LIYRHMKPENFLIGWSGNKAQQVTHII

Parental  DFGLAKEYID-PETKKHIPYREHKSLTGTARYMSINTHLGKEQSRRDD-LEALGHMFMYFLRGSLPWQGL
          DFGL.K..I.....K..........LTGTARYMS.NTHLGKEQSRR.D.L.AL.HMFMYFLRG.LPW..L
Retrocopy DFGLTKV*IY*SRDKETYTIQRTRILTGTARYMSLNTHLGKEQSRRADLLGALSHMFMYFLRGGLPWHAL

Parental  KADTLKE
          K..TL.E
Retrocopy KVHTLRE

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	3.31 RPM
SRP017611_kidney	0.07 RPM	1.88 RPM
SRP017611_liver	0.27 RPM	1.95 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2267 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2267 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2267 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010080	3 retrocopies	retro_chof_1577, retro_chof_2058, retro_chof_216,
Dasypus novemcinctus	ENSDNOG00000018857	1 retrocopy	retro_dnov_2386,
Rattus norvegicus	ENSRNOG00000016620	1 retrocopy	retro_rnor_2267 ,
Rattus norvegicus	ENSRNOG00000016677	1 retrocopy	retro_rnor_2189,
Tupaia belangeri	ENSTBEG00000003013	1 retrocopy	retro_tbel_17,