RetrogeneDB ID: retro_rnor_1660

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:176377286..176377961(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gnb1
• Ensembl ID: ENSRNOG00000016638
• Aliases: None
• Description: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 [Source:UniProtKB/Swiss-Prot;Acc:P54311]

Sequence

>retro_rnor_1660
GGCCTGGATAACATCTGCTCCATTTACAATCTGACAACTCGTGAAGGAAATGTGCGTGTGAGTCGTGAGCTGGCAGGACA
TACAGGTTATCTATCCTGTTGCCGGTTCCTGGATGACAATCAGATAGTTACCAGTTCTGGAGACACCACATGTGCCCTGT
GGGACATCGAGACTGGCCAGCAGACAACCACGTTTACTGGACACACTGGAGATGTCATGAGCCTGTCTCTTGCTCCTGAC
ACCAGACTGTTTGTCTCTGGTGCTTGCGATGCTTAGGCCAAGCTCTGGGATGTCCGAGAAGGGATGTGCCGGCAGACCTT
TGCAGGACACGAGTCTGACATCAATGCCATATGTTTCTTTCCCAATGGCAATGCCTTTGCCACTGGCTCAGACGATGCTA
CATGCAGGCTGTTTGACCTTCGTGGAGACCAGGAGCTCATGACCTACTCCCATGACAACATTATCTGTGGTATCACATCT
GTTTCCTTCTCCAAGAGTGGCCGCCTCCTCCTCGCTGGCTATAACGACTTCAACTGTAATGTCTGGGATGCACTCAAAGC
TGACAGAGCAGGTGTCCTAGCTGGACATGACAACCGAGTCAGCTGCTTGGGGGTGAGTGATGATGGCATGGCTGTGGCAA
CAGGATCCTGGGACAGCTTCCTCAAGATCTGGAAC

Alignment

ORF - retro_rnor_1660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.33 %
• Parental protein coverage: 66.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTG
          GLDNICSIYNL.TREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTG
Retrocopy GLDNICSIYNLTTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTG

Parental  DVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDL
          DVMSLSLAPDTRLFVSGACDA.AKLWDVREGMCRQTF.GHESDINAICFFPNGNAFATGSDDATCRLFDL
Retrocopy DVMSLSLAPDTRLFVSGACDA*AKLWDVREGMCRQTFAGHESDINAICFFPNGNAFATGSDDATCRLFDL

Parental  RADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGM
          R.DQELMTYSHDNIICGITSVSFSKSGRLLLAGY.DFNCNVWDALKADRAGVLAGHDNRVSCLGV.DDGM
Retrocopy RGDQELMTYSHDNIICGITSVSFSKSGRLLLAGYNDFNCNVWDALKADRAGVLAGHDNRVSCLGVSDDGM

Parental  AVATGSWDSFLKIWN
          AVATGSWDSFLKIWN
Retrocopy AVATGSWDSFLKIWN

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	0.58 RPM	287.80 RPM
SRP017611_kidney	0.28 RPM	87.51 RPM
SRP017611_liver	0.07 RPM	33.01 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1660 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1660 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1660 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019216	1 retrocopy	retro_cfam_1083,
Echinops telfairi	ENSETEG00000020012	1 retrocopy	retro_etel_1984,
Rattus norvegicus	ENSRNOG00000016638	1 retrocopy	retro_rnor_1660 ,