RetrogeneDB ID: retro_rnor_1341

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:29244058..29244675(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLVRB
• Ensembl ID: ENSRNOG00000024410
• Aliases: None
• Description: flavin reductase [Source:RefSeq peptide;Acc:NP_001099706]

Sequence

>retro_rnor_1341
GTGACTGTCAAGAAGAGCGTGATCTTCTGTGCCACCGGCAGAACCGGGCTCACCACACTGGCGCAGGCAGTGCAAGCAGG
TTACAAGGTGACAGTTCTGGTTCGAGACTCCAGCAGGCTGCCGTCAGAGGGGCCCCAGCCAGCCCACATGGTGGTAGGAG
ATGTTCAGCAGGCAGCCGATGTGGACAAGACTGTGGCTGGGCAGGATGCCGTCATCATGCTACTAGGCATTGGCAACGAC
CTCAGTCCCACTACAGGAATGTCCGAGGGCACCTGGGACATTGTGGCAGCCATGAAGGCACATGGAGTGGACAAGGCCGT
GGCCTGCACCTTGGCCCTCCTACTCTGGGACCCGATCAAGTGCTCCCACGCCTACAGGACCTGACCGATGACCACATTAG
GATGCATAAGATTCTGCAGGAGTCGGGTCTGAAATGCGTGGCTGTAATGCCCCCACACATTGGGTACCAACCACTAACCG
GGGCCTACACAGTGACCCTGGATGGACAAGGGCCCTCGAGGGTCATATCCAAGCATGACCAGGGCCACTTCATGCTTCTG
TGCCTCACCGCCCATGAGTAAGACAGACACAAGACCTACCCCTCCCACCAGTATGAC

Alignment

ORF - retro_rnor_1341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.02 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVKKIAIFGATGRTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPQPAHVVVGDVLQAGDVDKTVAGQDA
          ..VKK..IF.ATGRTGLTTLAQAVQAGY.VTVLVRDSSRLPSEGPQPAH.VVGDV.QA.DVDKTVAGQDA
Retrocopy VTVKKSVIFCATGRTGLTTLAQAVQAGYKVTVLVRDSSRLPSEGPQPAHMVVGDVQQAADVDKTVAGQDA

Parental  VIVLLGTGNDLSPTTVMSEGTRNIVAAMKAHGVDKVVACTSAFLLWDPSK-VPPRLQDVTDDHIRMHKIL
          VI.LLG.GNDLSPTT.MSEGT..IVAAMKAHGVDK.VACT.A.LLWDP.K.V.PRLQD.TDDHIRMHKIL
Retrocopy VIMLLGIGNDLSPTTGMSEGTWDIVAAMKAHGVDKAVACTLALLLWDPIK<VLPRLQDLTDDHIRMHKIL

Parental  EESGLKYVAVMPPHIGDQPLTGAYTVTLDGRGPSRVISKHDLGHFMLRCLTTHEYDGQKTYPSHQYD
          .ESGLK.VAVMPPHIG.QPLTGAYTVTLDG.GPSRVISKHD.GHFML.CLT.HE.D..KTYPSHQYD
Retrocopy QESGLKCVAVMPPHIGYQPLTGAYTVTLDGQGPSRVISKHDQGHFMLLCLTAHE*DRHKTYPSHQYD

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	14.02 RPM
SRP017611_kidney	12.28 RPM	15.00 RPM
SRP017611_liver	7.06 RPM	45.72 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1341 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1341 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1341 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010508	2 retrocopies	retro_btau_289, retro_btau_718,
Rattus norvegicus	ENSRNOG00000024410	1 retrocopy	retro_rnor_1341 ,
Ictidomys tridecemlineatus	ENSSTOG00000002958	1 retrocopy	retro_itri_1079,
Tupaia belangeri	ENSTBEG00000015357	2 retrocopies	retro_tbel_2799, retro_tbel_4031,