RetrogeneDB ID: retro_rnor_256

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:62894478..62895150(+)
• Located in intron of: ENSRNOG00000042668

Retrocopy information

• Ensembl ID: ENSRNOG00000004453
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Styx
• Ensembl ID: ENSRNOG00000007956
• Aliases: None
• Description: serine/threonine/tyrosine interacting protein [Source:RefSeq peptide;Acc:NP_001258470]

Sequence

>retro_rnor_256
ATGGAGGACGTGAAACTGGAGTTCCCCTCGCTCCCGCAGTGCAAAGACGACGTCGAGGAGTGGACTTACCCTATGAGACG
AGAGATGCAGGAAGTTTTGCCTGGATTGTTCTTAGGCCCCTACTCTTCTGCTATGAAAAGCAAGCTACCTATACTGCAGA
AACATGGCATAACTCATATAATTTGCATACGGCAAAATATTGAAGCAAACTTTATTAAACCAAACTTTCAACAATTATTT
AGGTATCTAGTCTTGGATATTGCTGATAATCCAGTTGAAAACATAATACGTTTTTTCCCTATGACTAAAGAGTTTATTGA
TGGAAGCTTACAAAATGGAGGAAAAGTTCTCGTCCATGGGAATGCAGGTATCTCTAGAAGTGCCGCCTTTGTTATTGCAT
ACATCATGGAGACATTTGGGATGAAGTACAGAGATGCATTTGCTTGTGTCCAAGAAAGGAGATTTTGTATTAATCCTAAT
GCTGGATTTGTCCACCAACTTCAGGAATATGAAGCCATCTACTTAGCAAAATTAACAATACAGATGATGTCACCACTCCA
GATAGAAAGGTCTTTATCTGTTCATTCTGGTACTACAGGTAGTGTGAAGAGAACATACGAAGATGATGGTGACTTTGGGA
ACATGCAAGTGGCAACCGCACAGAATGGCTGA

Alignment

ORF - retro_rnor_256 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDVKLEFPSLPQCKDDAEEWTYPMRREMQEVLPGLFLGPYSSAMKSKLPILQKHGITHIICIRQNIEAN
          MEDVKLEFPSLPQCKDD.EEWTYPMRREMQEVLPGLFLGPYSSAMKSKLPILQKHGITHIICIRQNIEAN
Retrocopy MEDVKLEFPSLPQCKDDVEEWTYPMRREMQEVLPGLFLGPYSSAMKSKLPILQKHGITHIICIRQNIEAN

Parental  FIKPNFQQLFRYLVLDIADNPVENIIRFFPMTKEFIDGSLQNGGKVLVHGNAGISRSAAFVIAYIMETFG
          FIKPNFQQLFRYLVLDIADNPVENIIRFFPMTKEFIDGSLQNGGKVLVHGNAGISRSAAFVIAYIMETFG
Retrocopy FIKPNFQQLFRYLVLDIADNPVENIIRFFPMTKEFIDGSLQNGGKVLVHGNAGISRSAAFVIAYIMETFG

Parental  MKYRDAFAYVQERRFCINPNAGFVHQLQEYEAIYLAKLTIQMMSPLQIERSLSVHSGTTGSVKRTYEDDD
          MKYRDAFA.VQERRFCINPNAGFVHQLQEYEAIYLAKLTIQMMSPLQIERSLSVHSGTTGSVKRTYEDD.
Retrocopy MKYRDAFACVQERRFCINPNAGFVHQLQEYEAIYLAKLTIQMMSPLQIERSLSVHSGTTGSVKRTYEDDG

Parental  DFGNMQVATAQNG
          DFGNMQVATAQNG
Retrocopy DFGNMQVATAQNG

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	0.07 RPM	2.01 RPM
SRP017611_kidney	0.07 RPM	5.65 RPM
SRP017611_liver	0.00 RPM	3.56 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_256 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_256 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016631	9 retrocopies	retro_dnov_1713, retro_dnov_1720, retro_dnov_1914, retro_dnov_2138, retro_dnov_2186, retro_dnov_2218, retro_dnov_2221, retro_dnov_461, retro_dnov_66,
Echinops telfairi	ENSETEG00000000561	1 retrocopy	retro_etel_1881,
Monodelphis domestica	ENSMODG00000029372	1 retrocopy	retro_mdom_44,
Mus musculus	ENSMUSG00000053205	1 retrocopy	retro_mmus_96,
Oryctolagus cuniculus	ENSOCUG00000029442	1 retrocopy	retro_ocun_1555,
Ochotona princeps	ENSOPRG00000016123	1 retrocopy	retro_opri_976,
Rattus norvegicus	ENSRNOG00000007956	1 retrocopy	retro_rnor_256 ,
Rattus norvegicus	ENSRNOG00000018218	2 retrocopies	retro_rnor_858, retro_rnor_887,
Ictidomys tridecemlineatus	ENSSTOG00000014504	1 retrocopy	retro_itri_1365,
Vicugna pacos	ENSVPAG00000012229	1 retrocopy	retro_vpac_464,