RetrogeneDB ID: retro_rnor_1380

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:2108610..2109082(-)
• Located in intron of: ENSRNOG00000013281

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam100b
• Ensembl ID: ENSRNOG00000010029
• Aliases: None
• Description: Protein Fam100b [Source:UniProtKB/TrEMBL;Acc:D3ZX60]

Sequence

>retro_rnor_1380
GAGCTGCGGCACGACGTCATGATCCACCAGTTCGTGCTGGCCGTGGGTTGCGTGGCCGACCAGGCGCAGCAGCTGCTGCA
AGCGGCCCACTGGCAGTTCCAGACCGCCCTAAGCACGTTCTTTCAAGAAAGCAACATTCCCAACAGCCACCACCACCCGC
AGTTGATGTGCACTCCCAGCAACACCCCTGCCACACCACCCAACTTCCCTGATGCGCTGGCCATGTTCTCCAAGCTTCAA
ACCTCTGAGGGCCTGCAGAGCAGCAGCAGCCCCATGACAGCAGTGGCCTGCTCCCCTCCCCCTGCAAACTTAAGCCCCTT
CTGGGCCGCATCCCCACCCAACACCAGGTGCCCTGGATCCCGCCCTCTTCCCCCAACACCTTCCATCCTCACTGCCCACA
GCCCACGTGGCCCCCGGAGCATCACAGGGGGGCGGCCCTCAGAAAGCCATGGCAGCCATGGATGGCCAGAGA

Alignment

ORF - retro_rnor_1380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.88 %
• Parental protein coverage: 96.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELRHQVMINQFVLAAGCAADQAQQLLQAAHWQFETALSTFFQESNIPNSHHHPQMMCTPSNTPATPPNFP
          ELRH.VMI.QFVLA.GC.ADQAQQLLQAAHWQF.TALSTFFQESNIPNSHHHPQ.MCTPSNTPATPPNFP
Retrocopy ELRHDVMIHQFVLAVGCVADQAQQLLQAAHWQFQTALSTFFQESNIPNSHHHPQLMCTPSNTPATPPNFP

Parental  DALAMFSKLRTSEGLQSSSSPMTAVACS-PPANFSPFWAASPPN-HQVPWIPPSSPNTFHLHCPQPTWP-
          DALAMFSKL.TSEGLQSSSSPMTAVACS.PPAN.SPFWAASPPN.HQVPWIPPSSPNTFH.HCPQPTWP.
Retrocopy DALAMFSKLQTSEGLQSSSSPMTAVACSPPPANLSPFWAASPPN<HQVPWIPPSSPNTFHPHCPQPTWP<

Parental  PGASQGGAPQKAMAAMDGQR
          PGASQGG.PQKAMAAMDGQR
Retrocopy PGASQGGGPQKAMAAMDGQR

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	10.35 RPM
SRP017611_kidney	0.07 RPM	30.29 RPM
SRP017611_liver	0.13 RPM	8.14 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1380 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1380 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000050628	1 retrocopy	retro_mmus_241,
Rattus norvegicus	ENSRNOG00000010029	1 retrocopy	retro_rnor_1380 ,