RetrogeneDB ID: retro_rnor_1179

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:14713927..14714519(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000022621
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eci2
• Ensembl ID: ENSRNOG00000016369
• Aliases: Eci2, Peci
• Description: Enoyl-CoA delta isomerase 2, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5XIC0]

Sequence

>retro_rnor_1179
CACAGCAGTGGGAGTGATTTGACTAACTTCACTAGTGCCACTGGGGGAATAGAGGAGGCAGTTAATGAGGGTGTGTGGAA
CCGAGAGAATTTGTAAACAGTTTTATAGACTTTCCCAAGCCTCTTGTTGCAGTAGTAAAAGACCCAGCTGTGGGAATATC
TGTCACTATTCTGAGACTATTCGATACTGTCTATGCATTGGACAGGACAACGTTTCATACTCCGTTCAGCCACCTTGGCC
AGAGCCCGGAGGCATGCTCCTCTTACTTGTTTCCGAATATGATGGACTCAGCAAAGGCAACTGAGATGCTTCTCTTTGGG
AAGAGGGTCACAGAAAGAGAGGCTTGGGCTCAATGCCTTGTCACTGAAGTTTTCCCTGAAAGCACTTTTGAAACAGAAGT
CTGGACAAGGCTGAAAGCATATGCGAAGCTCCTGTCAAACGCCAGGAGAATTTCCAAAGGGTTAATCAGAAAAATTGAAA
AAGAAAATCTCCATACAATAACGCTGAAGAATGCACTACTCTCTGAGCAAGGTGGCTGTCAGAGGAACGCATAAACGCGA
TCTTGAGCTTTGTATCCAGAAAACCAAAGCTG

Alignment

ORF - retro_rnor_1179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.5 %
• Parental protein coverage: 50.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YSSGNDLTNFTSASGGMEEAANKGA-IVLREFVNTFIDFPKPLVAVVNGPAVGISVTLLGLFDAVYASDR
          .SSG.DLTNFTSA.GG.EEA.N.G.....REFVN.FIDFPKPLVAVV..PAVGISVT.L.LFD.VYA.DR
Retrocopy HSSGSDLTNFTSATGGIEEAVNEGV<VEPREFVNSFIDFPKPLVAVVKDPAVGISVTILRLFDTVYALDR

Parental  ATFHTPFSHLGQSPEACSSYTFPKMMGSAKAAEMLLFGKKLTAREAWAQGLVTEVFPESTFETEVWTRLK
          .TFHTPFSHLGQSPEACSSY.FP.MM.SAKA.EMLLFGK..T.REAWAQ.LVTEVFPESTFETEVWTRLK
Retrocopy TTFHTPFSHLGQSPEACSSYLFPNMMDSAKATEMLLFGKRVTEREAWAQCLVTEVFPESTFETEVWTRLK

Parental  TYAKLPPNSMRISKELIRKNEKEKLHAV-NEEECTTLRARWLSEECINAIMSFVTRKPKL
          .YAKL..N..RISK.LIRK.EKE.LH...N.EECTTL.ARWLSEE.INAI.SFV.RKPKL
Retrocopy AYAKLLSNARRISKGLIRKIEKENLHTI<NAEECTTL*ARWLSEERINAILSFVSRKPKL

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	17.18 RPM
SRP017611_kidney	0.00 RPM	85.27 RPM
SRP017611_liver	0.00 RPM	111.14 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1179 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1179 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009409	1 retrocopy	retro_cfam_536,
Choloepus hoffmanni	ENSCHOG00000009239	1 retrocopy	retro_chof_25,
Procavia capensis	ENSPCAG00000008568	1 retrocopy	retro_pcap_71,
Rattus norvegicus	ENSRNOG00000016369	1 retrocopy	retro_rnor_1179 ,
Tupaia belangeri	ENSTBEG00000015862	2 retrocopies	retro_tbel_2398, retro_tbel_814,