RetrogeneDB ID: retro_rnor_701

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:65485502..65485892(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nsmce2
• Ensembl ID: ENSRNOG00000003964
• Aliases: Nsmce2, RGD1305156
• Description: E3 SUMO-protein ligase NSE2 [Source:UniProtKB/Swiss-Prot;Acc:Q4V8A0]

Sequence

>retro_rnor_701
TTGAGTCGTGAGTACAGTATGGATAAGGCCCTGGTTGACTTTGCTAAAATGGGTTGGGAACTAAACCATTATGTTAAGGC
TGCCCAACCTATAATAAGTCATGTAAAAGAAGGATGTCCAGAAAAAGTATGACATTTAACATGACTAGCGGAGAAGAAAG
GTTTGATTTTTCAGGATAAGCATTCTGATGCCGACTTTAACGGCAGGGAGAAGTTTGTGCAGGTTAAGCAACAGCTGAAG
AAGCACTGTGGTCTGTATGCAGACAGAGAGAATGATGGGACAGAAGGAGCCGATAAGGATACGATTTTGATCCAGATGCA
GACCAATTTCATCTGCCCTATAACACAGATGGAAATGAAGAAATCACTAAAAAACAACGTATGGCCGCAC

Alignment

ORF - retro_rnor_701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.41 %
• Parental protein coverage: 53.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSSEYSMDKAMVEFAKMDRELNHYVKAVQSTINHVKEERPEKVPDLKLLVEKKFLALQDKNSDADFKENE
          .S.EYSMDKA.V.FAKM..ELNHYVKA.Q..I.HVKE..PEKV..L..L.EKK.L..QDK.SDADF...E
Retrocopy LSREYSMDKALVDFAKMGWELNHYVKAAQPIISHVKEGCPEKV*HLT*LAEKKGLIFQDKHSDADFNGRE

Parental  KFVQFKQQLRELKKQYGIHADRENDGIEGMDEDMIVTQSQTNFICPITQLEMKKPVKNKMCGH
          KFVQ.KQQL...KK..G..ADRENDG.EG.D.D.I..Q.QTNFICPITQ.EMKK..KN....H
Retrocopy KFVQVKQQL---KKHCGLYADRENDGTEGADKDTILIQMQTNFICPITQMEMKKSLKNNVWPH

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	9.56 RPM
SRP017611_kidney	0.00 RPM	12.91 RPM
SRP017611_liver	0.00 RPM	7.73 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_701 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_701 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_701 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009394	1 retrocopy	retro_btau_669,
Echinops telfairi	ENSETEG00000019897	1 retrocopy	retro_etel_1348,
Macaca mulatta	ENSMMUG00000003542	1 retrocopy	retro_mmul_1641,
Mus musculus	ENSMUSG00000059586	3 retrocopies	retro_mmus_1189, retro_mmus_1190, retro_mmus_3227,
Otolemur garnettii	ENSOGAG00000015798	1 retrocopy	retro_ogar_3039,
Rattus norvegicus	ENSRNOG00000003964	2 retrocopies	retro_rnor_2118, retro_rnor_701 ,
Tupaia belangeri	ENSTBEG00000005371	1 retrocopy	retro_tbel_3224,