RetrogeneDB ID: retro_rnor_850

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 12:901786..902089(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hspb11
• Ensembl ID: ENSRNOG00000010241
• Aliases: None
• Description: heat shock protein beta-11 [Source:RefSeq peptide;Acc:NP_001124474]

Sequence

>retro_rnor_850
ACCACAGGCACGGTTCCCAGGAGTTCCTTATTTGTTTCACAAACATGTCAAGATTGAAAATCTTGTGACCCAAAGTTACT
TAGTGCAGACCTTGAGGACTGAAAAGACCATGTGAAAAGAACCATTCGATTTTGAGCAGTGGGTTGAAAAATATCTAGAA
CTCGATGAAGAGGGGCGGCTTCAAACCCCTTCATGTTGTGGCATGAGATGGCCACTTCCTTGAGATTCACTCTTGTCTCA
GCCTTCAATCATCTTGCATCTGAACCTAGCATCCCTACAGAGGGACAAGCAGTCTCAAGTCTC

Alignment

ORF - retro_rnor_850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.55 %
• Parental protein coverage: 71.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TTGMFP-QEFIIC-FHKHVKIEKLVIQSYLVRTLRIEKTTSKEPLDFEQWVEKDL-VHTEGQLQNE-EIM
          TTG..P.QEF.IC.FHKHVKIE.LV.QSYLV.TLR.EKT..KEP.DFEQWVEK.L....EG.LQ......
Retrocopy TTGTVP<QEFLIC<FHKHVKIENLVTQSYLVQTLRTEKTM*KEPFDFEQWVEKYLELDEEGRLQTP>HVV

Parental  ARDGYATFL-RFIIVSAFDHFASVHSISAEGLTVSSL
          A.DG...FL.RF..VSAF.H.AS..SI..EG..VSSL
Retrocopy A*DGH--FL>RFTLVSAFNHLASEPSIPTEGQAVSSL

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	4.39 RPM
SRP017611_kidney	0.00 RPM	3.56 RPM
SRP017611_liver	0.00 RPM	1.82 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_850 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_850 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000284	3 retrocopies	retro_dnov_2439, retro_dnov_386, retro_dnov_514,
Rattus norvegicus	ENSRNOG00000010241	2 retrocopies	retro_rnor_849, retro_rnor_850 ,
Ictidomys tridecemlineatus	ENSSTOG00000002643	1 retrocopy	retro_itri_1217,
Tarsius syrichta	ENSTSYG00000012499	2 retrocopies	retro_tsyr_1813, retro_tsyr_697,