RetrogeneDB ID: retro_rnor_2192

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:172405163..172405476(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGD1311103
• Ensembl ID: ENSRNOG00000025957
• Aliases: Ooep, RGD1311103
• Description: None

Sequence

>retro_rnor_2192
CAGGAACTCAGCAATCCTGTGGTGCTCTACATGGAAGCCTGGGTGGCAGAAAGGACGATTGGCCCAGACCAAGCCGAAAT
CGCGGAAATAGAGTGGATGAGCCAGGCCTTGCTGAGATTGGACTCAGCCAGCTCTGGGAACCTAGCTGAAATCACCATCT
TTGGATGACTCAGTGCACAGACTCGAATGAAAAATATTCTCTTGAAAAATGGCGGCCTGGCGCCAAGAAAACGGAGTCCA
AAGAGCTATGAAGATGAAACAAGTTGAAGAGTTCTTGAAAGTCCGTGCCTCCTCAATTGTAAGCAACCCAAGT

Alignment

ORF - retro_rnor_2192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.57 %
• Parental protein coverage: 69.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QELSNPMVFYLESWVAERIIGSDQDEISEIEWMSQALLSVNLANSGKLAEITIYGRPSAQIRMKNILL-N
          QELSNP.V.Y.E.WVAER.IG.DQ.EI.EIEWMSQALL....A.SG.LAEITI.G..SAQ.RMKNILL..
Retrocopy QELSNPVVLYMEAWVAERTIGPDQAEIAEIEWMSQALLRLDSASSGNLAEITIFG*LSAQTRMKNILL>K

Parental  MVAWYKEDEVQRAVKLKQVEEFLKQHASSIITQAS
          M.AW..E..VQRA.K.KQVEEFLK..ASSI....S
Retrocopy MAAWRQENGVQRAMKMKQVEEFLKVRASSIVSNPS

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.07 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2192 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2192 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2192 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009962	1 retrocopy	retro_cjac_3033,
Homo sapiens	ENSG00000203907	3 retrocopies	retro_hsap_432, retro_hsap_4807, retro_hsap_543,
Gorilla gorilla	ENSGGOG00000016832	3 retrocopies	retro_ggor_2992, retro_ggor_422, retro_ggor_495,
Loxodonta africana	ENSLAFG00000012754	2 retrocopies	retro_lafr_412, retro_lafr_782,
Myotis lucifugus	ENSMLUG00000017174	2 retrocopies	retro_mluc_115, retro_mluc_252,
Macaca mulatta	ENSMMUG00000000416	2 retrocopies	retro_mmul_2561, retro_mmul_519,
Nomascus leucogenys	ENSNLEG00000001204	2 retrocopies	retro_nleu_2182, retro_nleu_717,
Oryctolagus cuniculus	ENSOCUG00000025904	1 retrocopy	retro_ocun_20,
Pan troglodytes	ENSPTRG00000029545	3 retrocopies	retro_ptro_3197, retro_ptro_329, retro_ptro_408,
Rattus norvegicus	ENSRNOG00000025957	1 retrocopy	retro_rnor_2192 ,
Tursiops truncatus	ENSTTRG00000001487	2 retrocopies	retro_ttru_1376, retro_ttru_1803,