RetrogeneDB ID: retro_rnor_505

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:180072588..180073144(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gnai2
• Ensembl ID: ENSRNOG00000016592
• Aliases: Gnai2, Galphai2
• Description: Guanine nucleotide-binding protein G(i) subunit alpha-2 [Source:UniProtKB/Swiss-Prot;Acc:P04897]

Sequence

>retro_rnor_505
AATGACTATATCCCTATGCAGCAGGATGTGCTGCGGACCCGTGTGAAGACCACAGGTATCGTTGAAACACACTTCACCTT
CAAGGACTTACACTTTAAGATGTTTGATGTGGGTGGTCAGCGATCTGAGCAGAAGAAGTAGATCCACTGCTTTGAGGGTG
TCACGGCCATTATCTTCTGTGTCGCCTTGAGCGCCTATGACTTGGTTCTGGCTAGGATGAGGAGATGAATCGCATGCATG
AGAGCGTGAAGCTGTTTGATAGCATCTGCAATAACAAGTGATTCACAGACACCTCCATCATCCTCTTCCTCAACAAGAAG
GACCTGATCACACAGAGCTCCTGACCATCTGTTTCCCTGAGTACACAGGGGCTAACAAGTATGATGAGGTAGCCAGCTAC
ATCCAGAGCAAGTTTGAGGACTTGAATAAATGCAAAGACACCAAGGAGATCTACACACATTTCACGTGTGCCACCAACAC
CAAGAACGTGCAGTTTGTGTTTGATGCCATCACTGACGTCATCATCAAGAACAACCTGAAGGACTGTGGCTTCTTC

Alignment

ORF - retro_rnor_505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.1 %
• Parental protein coverage: 53.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SDYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSAYDLVL
          .DYIP.QQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSE.KK.IHCFEGVTAIIFCVALSAYDLVL
Retrocopy NDYIPMQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSEQKK*IHCFEGVTAIIFCVALSAYDLVL

Parental  AE-DEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITQSP-LTICFPEYTGANKYDEAASY
          A..DEEMNRMHES.KLFDSICNNK.FTDTSIILFLNKKDL....ITQS..LTICFPEYTGANKYDE.ASY
Retrocopy AR<DEEMNRMHESVKLFDSICNNK*FTDTSIILFLNKKDL----ITQSS<LTICFPEYTGANKYDEVASY

Parental  IQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
          IQSKFEDLNK.KDTKEIYTHFTCAT.TKNVQFVFDA.TDVIIKNNLKDCG.F
Retrocopy IQSKFEDLNKCKDTKEIYTHFTCATNTKNVQFVFDAITDVIIKNNLKDCGFF

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	197.86 RPM
SRP017611_kidney	0.00 RPM	165.17 RPM
SRP017611_liver	0.00 RPM	51.91 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_505 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_505 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_505 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000005305	1 retrocopy	retro_cint_14,
Callithrix jacchus	ENSCJAG00000004925	1 retrocopy	retro_cjac_1091,
Ciona savignyi	ENSCSAVG00000001800	1 retrocopy	retro_csav_19,
Felis catus	ENSFCAG00000007008	1 retrocopy	retro_fcat_157,
Otolemur garnettii	ENSOGAG00000012525	1 retrocopy	retro_ogar_1470,
Rattus norvegicus	ENSRNOG00000016592	1 retrocopy	retro_rnor_505 ,