RetrogeneDB ID: retro_rnor_1864

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:10713034..10713807(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Slbp
• Ensembl ID: ENSRNOG00000037162
• Aliases: None
• Description: histone RNA hairpin-binding protein [Source:RefSeq peptide;Acc:NP_001124460]

Sequence

>retro_rnor_1864
ATGGTCTGCAGACCTAGAAGCCCACCCTGTTATGGGAGTCGCTGTGACGGCGGTGCAAGTCCGAAGTCCCCTATGAGATG
GAGTCTCGGACAGAAGTGCAGAGCAGATGGAAGGGACTGGAAGCCTGAGGACTCCAAGGAAGGCGAGCTCCAGACTGAGG
ACCATCAACCTAGAAGCTTTACAACTCCTGAAGGCCATAAGCCCCTTTCTAGATGTTCTGACTGGGCAAGCGCAGTTGAA
GAAGATGACATGAGGACCAGAGTTAACAAAGAGATTGCAAGGTACAAAAGAAAGCTACTCATAAATGACTTTGGAAGACA
GAGAAAATCATCATCGAGAAGTTCTGATTCAAAGAAGTCTGTGTCTTCGGTGCCTACTGACATGGAGACAGATGCAAGTG
TCTTGATGGAAGGCAGAAGCAGATCAACTACAGGAAGAACACTATGGCCTATGATCAATACATTAAAGAGATGCCCAGAC
ACCTGTGATATCCCAGGACCTCCAACAAATTTAAGAAATATAGCCTGTGGTCATGGGACCAACAGATTAAACTCTGGAAG
GTGGCTTTGCATTTTTGGGATCCTCCTGCTGAAGAAGGGTATGATTTGCAAGAAATACAACATGTAGATCTTGGGGAAAT
GGAGACAGAATTCACAGAAAGCAGTTGTGAGTCCCAGACAAGTTCACAGAATAACTTTGATGTATATGCTGGCACACTCA
CCAAAGTCAGACATGTGGATTGCCAAGTGGAGGATGAGTTTGATTTGGAAGCT

Alignment

ORF - retro_rnor_1864 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.17 %
• Parental protein coverage: 95.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MACRPRSPPRYGSRRDGGASPRSPARWSLGRKRRADGRDRKPEDSEEGELQTADHRPESFTTPEGHKPRS
          M.CRPRSPP.YGSR.DGGASP.SP.RWSLG.K.RADGRD.KPEDS.EGELQT.DH.P.SFTTPEGHKP.S
Retrocopy MVCRPRSPPCYGSRCDGGASPKSPMRWSLGQKCRADGRDWKPEDSKEGELQTEDHQPRSFTTPEGHKPLS

Parental  RCSDWASAVEEDEMRTRVNKEIARYKRKLLINDFGRERKSSSGSSDSKESVSSVPADVETDESVLMR-RQ
          RCSDWASAVEED.MRTRVNKEIARYKRKLLINDFGR.RKSSS.SSDSK.SVSSVP.D.ETD.SVLM..RQ
Retrocopy RCSDWASAVEEDDMRTRVNKEIARYKRKLLINDFGRQRKSSSRSSDSKKSVSSVPTDMETDASVLME<RQ

Parental  KQINYGKNTMAYDRYIKEVPRHLRQPGIHPRTPNKFKKYSRRSWDQQIKLWKVALHFWDPPAEEGCDLQE
          KQINY.KNTMAYD.YIKE.PRHL..P....RT.NKFKKYS..SWDQQIKLWKVALHFWDPPAEEG.DLQE
Retrocopy KQINYRKNTMAYDQYIKEMPRHL*YP----RTSNKFKKYSLWSWDQQIKLWKVALHFWDPPAEEGYDLQE

Parental  IQPVDLGEMETEFTESSSESQTSSQDNFDVYAGTPTKVRHVDCQVEDEFDLEA
          IQ.VDLGEMETEFTESS.ESQTSSQ.NFDVYAGT.TKVRHVDCQVEDEFDLEA
Retrocopy IQHVDLGEMETEFTESSCESQTSSQNNFDVYAGTLTKVRHVDCQVEDEFDLEA

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	12.87 RPM
SRP017611_kidney	0.00 RPM	17.03 RPM
SRP017611_liver	0.00 RPM	8.67 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1864 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1864 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1864 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001328	1 retrocopy	retro_btau_1456,
Cavia porcellus	ENSCPOG00000000031	1 retrocopy	retro_cpor_364,
Mus musculus	ENSMUSG00000004642	1 retrocopy	retro_mmus_1169,
Otolemur garnettii	ENSOGAG00000009750	1 retrocopy	retro_ogar_1463,
Pteropus vampyrus	ENSPVAG00000002807	2 retrocopies	retro_pvam_490, retro_pvam_941,
Rattus norvegicus	ENSRNOG00000037162	2 retrocopies	retro_rnor_1864 , retro_rnor_2016,
Tarsius syrichta	ENSTSYG00000000376	2 retrocopies	retro_tsyr_1595, retro_tsyr_482,
Tursiops truncatus	ENSTTRG00000010901	1 retrocopy	retro_ttru_10,