RetrogeneDB ID: retro_rnor_2566

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:47879434..47879953(+)
• Located in intron of: ENSRNOG00000026833

Retrocopy information

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

Parental gene information

• Parental gene symbol: Piga
• Ensembl ID: ENSRNOG00000003554
• Aliases: None
• Description: N-acetylglucosaminyl-phosphatidylinositol biosynthetic protein [Source:RefSeq peptide;Acc:NP_001102286]

Sequence

>retro_rnor_2566
CTTGGAGGAGAGGGACCAAAGAGTATAGTCTTGGAAGGAGTATAGGACAGATGCCAACTATATGACAGGTGCATCTTTTG
GGAGCTTTGGAATACAAAGCTATCAGAAATGTCTTAGTTCAAGGAATATTTTTTTAACACCTCCCTGTCTGAAGCCTTCT
GCATGGTAATCCTGGAAGCCACCAGCTGTGGTGTACAGGTTGTCAGCACCGAGGTTGGTGGGATTCTGGAAGTCTTTTCA
GAGAACCTTATTATTTTAGGTGAACCTGCAGTAAAATCTTTGTGTGAAGGGCTAGAAAAAGCTGTTTCCCAAGTGAAGTT
GGGGACATTGCCAGCTCCTGAAAACATCCACAGTATAGTAAAGGTGCTCTCCACCTGGTGGGGTGTGGCAGAGAGGACTG
AGGTGTACAGGATAGTGAATGGAACCGTGCTGCTGATGCACCAGAGGCTGAACTGGCTCACCTCTCACTGTGGCCCAGTT
ACAGGCCAGTTTTGCTTTGCTGGCTGTGCTCAGCTATCT

Alignment

ORF - retro_rnor_2566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.27 %
• Parental protein coverage: 69.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IGGEGPKRIILEEVRERYQLHDR-VQLLGALEHKDVRNVLVQG-HIFL-NTSLTEAFCMAIVEAASCGLQ
          .GGEGPK.I.LE.V..R.QL.DR.V.LLGALE.K..RNVLVQG..IFL.NTSL.EAFCM.I.EA.SCG.Q
Retrocopy LGGEGPKSIVLEGV*DRCQLYDR<VHLLGALEYKAIRNVLVQG<NIFL<NTSLSEAFCMVILEATSCGVQ

Parental  VVSTKVGGIPEVLPENLIILCEPSVKSLCEGLEKAIFQVKSGTLPAPENIHNVVKTFYTWRNVAERTEKV
          VVST.VGGI.EV..ENLIIL.EP.VKSLCEGLEKA..QVK.GTLPAPENIH..VK...TW..VAERTE.V
Retrocopy VVSTEVGGILEVFSENLIILGEPAVKSLCEGLEKAVSQVKLGTLPAPENIHSIVKVLSTWWGVAERTE-V

Parental  YERVSKESVLPMHKRLDRLISHCGPVTG-YIFALLAVLS
          Y.R.....VL.MH.RL..L.SHCGPVTG...FA..A.LS
Retrocopy Y-RIVNGTVLLMHQRLNWLTSHCGPVTGQFCFAGCAQLS

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	4.82 RPM
SRP017611_kidney	0.00 RPM	3.98 RPM
SRP017611_liver	0.00 RPM	1.88 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2566 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2566 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006415	1 retrocopy	retro_chof_2311,
Homo sapiens	ENSG00000165195	1 retrocopy	retro_hsap_1050,
Gorilla gorilla	ENSGGOG00000007293	1 retrocopy	retro_ggor_828,
Nomascus leucogenys	ENSNLEG00000009352	1 retrocopy	retro_nleu_2070,
Ochotona princeps	ENSOPRG00000015381	1 retrocopy	retro_opri_1065,
Pongo abelii	ENSPPYG00000020142	1 retrocopy	retro_pabe_876,
Pan troglodytes	ENSPTRG00000021684	1 retrocopy	retro_ptro_716,
Rattus norvegicus	ENSRNOG00000003554	1 retrocopy	retro_rnor_2566 ,