RetrogeneDB ID: retro_rnor_1749

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:1126677..1127106(-)
• Located in intron of: ENSRNOG00000048084

Retrocopy information

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

Parental gene information

• Parental gene symbol: D17Wsu92e
• Ensembl ID: ENSRNOG00000038883
• Aliases: LOC294154, RGD1310148
• Description: DNA segment, Chr 17, Wayne State University 92, expressed [Source:MGI Symbol;Acc:MGI:106281]

Sequence

>retro_rnor_1749
TCAATCAGTGTGCCCTCCATGTCTTTTGTTGAAGATGTCACCATAGGAGAAAGAGAGTCAATATCCCCCGATATCCAGTT
CATAAAAACACGGCCAATCCAGAATTCTGGGGCAGAAGCCTGTCTTCCAGGGATTTGTCGTAAATATGTTGAGGGAGACC
AGTTTGGACATGTGAACATGGTGATGGTGAGATCACTAGAGCCCCAAGAGATTGCAGATGTCAGCGTCCAGATGTGCAGG
CGCAGCAGAGCAGGAATATACCAGGGACAGTGGTGGATGTGCACTGCTACTGGACTCTACTATGGAGATGTTATCTGGGT
GATTCTCATTGTGGAGTTGGGTGAACTTTTTAGAGTAATACAGAGGCTGTCATCTTTTGAAACAGAATTCAACACACGGT
CACACCATCACAAGGTAGACGGAAACTTC

Alignment

ORF - retro_rnor_1749 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.62 %
• Parental protein coverage: 66.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVSVPSMSFVEDVTIGEGESIPPDTQFIKTWRIQNSGAEAWPPGVCLKYVGGDQFGHVNMVMVRSLEPQE
          ..SVPSMSFVEDVTIGE.ESI.PD.QFIKT..IQNSGAEA..PG.C.KYV.GDQFGHVNMVMVRSLEPQE
Retrocopy SISVPSMSFVEDVTIGERESISPDIQFIKTRPIQNSGAEACLPGICRKYVEGDQFGHVNMVMVRSLEPQE

Parental  IADVSVQMCSPSRAGMYQGQWRMCTATGLYYGDVIWVILSVEVGGLLGVTQQLSSFETEFNTQPHRKGLH
          IADVSVQMC..SRAG.YQGQW.MCTATGLYYGDVIWVIL.VE.G.L..V.Q.LSSFETEFNT..H.....
Retrocopy IADVSVQMCRRSRAGIYQGQWWMCTATGLYYGDVIWVILIVELGELFRVIQRLSSFETEFNTRSHHHKVD

Parental  GPY
          G..
Retrocopy GNF

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	249.98 RPM
SRP017611_kidney	0.00 RPM	348.91 RPM
SRP017611_liver	0.00 RPM	203.60 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1749 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1749 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1749 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000013442	1 retrocopy	retro_mmur_1615,
Oryctolagus cuniculus	ENSOCUG00000024862	2 retrocopies	retro_ocun_1955, retro_ocun_499,
Rattus norvegicus	ENSRNOG00000038883	2 retrocopies	retro_rnor_1748, retro_rnor_1749 ,
Tursiops truncatus	ENSTTRG00000007822	4 retrocopies	retro_ttru_1601, retro_ttru_1738, retro_ttru_1896, retro_ttru_827,