RetrogeneDB ID: retro_rnor_2233

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:94424015..94424712(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dnajb1
• Ensembl ID: ENSRNOG00000021824
• Aliases: None
• Description: dnaJ homolog subfamily B member 1 [Source:RefSeq peptide;Acc:NP_001101911]

Sequence

>retro_rnor_2233
ATCGCCGAAGCGTACCACCTGCTCAGCCACCCTCCCCAGGCATTAGATTTTTGACCGCTATGGAGAGGAAGACCTGAAGG
GAGGTCACCCCAGTGGCTGGAGCTGTGGAGGTGCTAACGGTACCTCTTTTAGCTACACATTCCATGGAGACCCTCATGAC
ATGTTTGATGAGTTCTTCGGTGGCAAGAACCCATTTGATACCTATTTTGGGTAGCGCAATGGGGAAGAAGGCATGGTAAT
CGATGACCCATTATCTGGCTTTCCAGTGGGTAAGGGTGGCTTCACCAATGTAAACTTTGGATTTTCCCACCCTACTCAAG
AGCCCACCAGAGGAAGCAAAATTCCCCAGTCACCCACGACCTTCAGGTCTCCCTTGAAGAGATCTACAGAGGCTGTACTA
AGAGGATGGAAATCCCTGACTAGCAACAAGCGGTTGAACCCTGATGGAAAGAGCATTAGAAATGAAGATAAGATCCTGAC
CATCGAAGTGAAGAGGGGCTGGAAAAAAGGGACCAAAATCACCTTTCCTAAGGAAGGGAACCAGACCTCTAACAACATTC
CAGCTGACATCATCTTTGTTTTAAAGGACAATCCACATAATATCTTCAAGAAAGCTGGTTCTGATGTCATTTATCCAGTC
AGGATTAGCCTTCAGAAGGCTCTCTGTGGTTGCAGTTTCAATATCCCTACTCTGGAT

Alignment

ORF - retro_rnor_2233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.53 %
• Parental protein coverage: 61.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IAEAYDVLSDPR-KREIFDRYGEEGLKGGGPSGGSSGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFF
          IAEAY..LS.P.....IFDRYGEE.LKGG.PSG.S.GGANGTSFSYTFHGDPH.MF.EFFGG.NPFDT.F
Retrocopy IAEAYHLLSHPP>RH*IFDRYGEEDLKGGHPSGWSCGGANGTSFSYTFHGDPHDMFDEFFGGKNPFDTYF

Parental  GQRNGEEGMDIDDPFSSFPMGMGGFTNMNFGRSRPTQEPTRKKQDPPVTHDLRVSLEEIYSGCTKKMK--
          G.RNGEEGM.IDDP.S.FP.G.GGFTN.NFG.S.PTQEPTR....P......R..L...........K..
Retrocopy G*RNGEEGMVIDDPLSGFPVGKGGFTNVNFGFSHPTQEPTRGSKIPQSPTTFRSPLKRSTEAVLRGWKSL

Parental  ISHKRLNPDGKSIRNEDKILTIEVKRGWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDV
          .S.KRLNPDGKSIRNEDKILTIEVKRGWK.GTKITFPKEG.QTSNNIPADI.FVLKD.PHNIFK..GSDV
Retrocopy TSNKRLNPDGKSIRNEDKILTIEVKRGWKKGTKITFPKEGNQTSNNIPADIIFVLKDNPHNIFKKAGSDV

Parental  IYPARISLREALCGCTVNVPTLD
          IYP.RISL..ALCGC..N.PTLD
Retrocopy IYPVRISLQKALCGCSFNIPTLD

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	40.77 RPM
SRP017611_kidney	0.00 RPM	42.36 RPM
SRP017611_liver	0.00 RPM	19.57 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2233 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2233 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2233 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004666	1 retrocopy	retro_cjac_463,
Pongo abelii	ENSPPYG00000009647	1 retrocopy	retro_pabe_2136,
Pan troglodytes	ENSPTRG00000010594	1 retrocopy	retro_ptro_1728,
Rattus norvegicus	ENSRNOG00000010353	6 retrocopies	retro_rnor_1680, retro_rnor_1930, retro_rnor_212, retro_rnor_2673, retro_rnor_60, retro_rnor_641,
Rattus norvegicus	ENSRNOG00000021824	1 retrocopy	retro_rnor_2233 ,