RetrogeneDB ID: retro_rnor_90

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:66991918..66992293(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000029737
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rps25
• Ensembl ID: ENSRNOG00000027503
• Aliases: None
• Description: 40S ribosomal protein S25 [Source:UniProtKB/Swiss-Prot;Acc:P62853]

Sequence

>retro_rnor_90
ATGCCGCCCAAAGACGACAAGAAGAAGAAGGATGCTGGAAAGTCCGCCAAAAAAGACAAAGACCCTATAAATAAATCTGG
TGGCAAGGCCAAAAAGAAGTGGTCCAAAGGCAAAGTTCTGGACAAGCTGAACAATCTCGTCCTGTTTGACAAAGCTACTT
ATGACAAACTTTGTAAGGAAGTTCCCAACTATAAGCTTATTACTCCATGTGTGGTCTCCGAGAGACTGAAGATTCTAGGT
TCCTTGGTCAGGGCAGCCCTTCAGGAGCTACTTAGTAAAGGACTTATCAAGCTGGTTTCAAAGCACAGAGCCCAAGTAAT
TTACACCAGAAACACAAAGGTTGGAGATGTCTCAGCTGCTAGTGAAGATGCATGA

Alignment

ORF - retro_rnor_90 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEVPNYKLITP
          MPPKDDKKKKDAGKSAKKDKDP.NKSGGKAKKK.WSKGKV.DKLNNLVLFDKATYDKLCKEVPNYKLITP
Retrocopy MPPKDDKKKKDAGKSAKKDKDPINKSGGKAKKK-WSKGKVLDKLNNLVLFDKATYDKLCKEVPNYKLITP

Parental  AVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA
          .VVSERLKI.GSL.RAALQELLSKGLIKLVSKHRAQVIYTRNTK.GD..AA.EDA
Retrocopy CVVSERLKILGSLVRAALQELLSKGLIKLVSKHRAQVIYTRNTKVGDVSAASEDA

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	48.24 RPM
SRP017611_kidney	0.00 RPM	72.64 RPM
SRP017611_liver	0.00 RPM	44.58 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_90 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_90 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_90 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027772	2 retrocopies	retro_btau_203, retro_btau_9,
Callithrix jacchus	ENSCJAG00000013691	1 retrocopy	retro_cjac_208,
Dasypus novemcinctus	ENSDNOG00000007880	7 retrocopies	retro_dnov_1092, retro_dnov_1566, retro_dnov_2219, retro_dnov_2593, retro_dnov_346, retro_dnov_877, retro_dnov_973,
Latimeria chalumnae	ENSLACG00000017531	4 retrocopies	retro_lcha_101, retro_lcha_118, retro_lcha_50, retro_lcha_72,
Macropus eugenii	ENSMEUG00000014185	3 retrocopies	retro_meug_1181, retro_meug_1562, retro_meug_174,
Mus musculus	ENSMUSG00000009927	15 retrocopies	retro_mmus_128, retro_mmus_1368, retro_mmus_1455, retro_mmus_1760, retro_mmus_1769, retro_mmus_1788, retro_mmus_2375, retro_mmus_2393, retro_mmus_2641, retro_mmus_2700, retro_mmus_2797, retro_mmus_3218, retro_mmus_336, retro_mmus_3523, retro_mmus_880,
Otolemur garnettii	ENSOGAG00000007265	3 retrocopies	retro_ogar_220, retro_ogar_257, retro_ogar_32,
Ochotona princeps	ENSOPRG00000016194	9 retrocopies	retro_opri_1099, retro_opri_1204, retro_opri_256, retro_opri_320, retro_opri_393, retro_opri_493, retro_opri_64, retro_opri_854, retro_opri_873,
Rattus norvegicus	ENSRNOG00000027503	5 retrocopies	retro_rnor_1430, retro_rnor_157, retro_rnor_893, retro_rnor_90 , retro_rnor_992,
Vicugna pacos	ENSVPAG00000000266	4 retrocopies	retro_vpac_106, retro_vpac_118, retro_vpac_337, retro_vpac_546,