RetrogeneDB ID: retro_rnor_2039

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:21895193..21895388(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif3k
• Ensembl ID: ENSRNOG00000020495
• Aliases: Eif3k, Eif3s12, PLAC-24
• Description: eukaryotic translation initiation factor 3 subunit K [Source:RefSeq peptide;Acc:NP_001099712]

Sequence

>retro_rnor_2039
CAAGCCTTGGTTGCGAACACGGACCTCCTGAAAGGCATAAGTGGCTTTGAAGACTCTGTCTGACAATTTATCTGCTGTGG
GGTGGGCAACATGCATCAGCACATTGACTGGTTGTTGGCTGAGAGGCTTGGAGATCTGACTGACAGCCAGCTGAAGGTGT
GGATGAGCACATATGGCTGGAGCACCGAGGAGACA

Alignment

ORF - retro_rnor_2039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.7 %
• Parental protein coverage: 61.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QALDENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEMLGDLTDNQLRVWMSKYGWSADES
          QAL..N.DLL.GI.GFEDSV..FIC..VG...QHID.WLLAE.LGDLTD.QL.VWMS.YGWS..E.
Retrocopy QALVANTDLLKGISGFEDSV*QFICCGVGNMHQHID-WLLAERLGDLTDSQLKVWMSTYGWSTEET

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	22.22 RPM
SRP017611_kidney	0.00 RPM	26.73 RPM
SRP017611_liver	0.00 RPM	11.36 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2039 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2039 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2039 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007594	3 retrocopies	retro_etel_1653, retro_etel_1868, retro_etel_5,
Gorilla gorilla	ENSGGOG00000016808	1 retrocopy	retro_ggor_2192,
Monodelphis domestica	ENSMODG00000013314	3 retrocopies	retro_mdom_1235, retro_mdom_1929, retro_mdom_781,
Otolemur garnettii	ENSOGAG00000026260	1 retrocopy	retro_ogar_413,
Pongo abelii	ENSPPYG00000025857	4 retrocopies	retro_pabe_2342, retro_pabe_2555, retro_pabe_2610, retro_pabe_2673,
Rattus norvegicus	ENSRNOG00000020495	3 retrocopies	retro_rnor_1128, retro_rnor_2039 , retro_rnor_513,
Sarcophilus harrisii	ENSSHAG00000005313	1 retrocopy	retro_shar_689,