RetrogeneDB ID: retro_rnor_609

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:150733376..150733672(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Scoc
• Ensembl ID: ENSRNOG00000003853
• Aliases: None
• Description: Short coiled-coil protein [Source:UniProtKB/Swiss-Prot;Acc:Q5RJZ6]

Sequence

>retro_rnor_609
GACCTTTCATTAACGAGTTTGAATTCAATAACTGAAAGTCTGTTAGTCAAGATGATGAATGCTGATATGGATACAGTTGA
TGCTGAAAATCAATGGAACTGGAAGAAAAGACTTGACTTATCAATCAGGTGTTGCATCTCCAGCACACACTTGAAGATCT
TTCTGCAAGAGTAGATGCAGTTAAGGAAAAAAATCTGAAGATAAAATCAGATAATCAAGTTATTGAACAACATATAGAAA
ACCTCATGTCTACTTCTAGTTTTACAAACAGCTGATGCAAAAAGCAAAAGAAACAA

Alignment

ORF - retro_rnor_609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.0 %
• Parental protein coverage: 81.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DHSLKSLHSGAERLFPKMMNADMDAVDAENQ-VELEEKTRLINQVLELQHTLEDLSARVDAVKEENLKLK
          D.SL.SL.S..E.L..KMMNADMD.VDAENQ..ELEEKT.LINQVL.LQHTLEDLSARVDAVKE.NLK.K
Retrocopy DLSLTSLNSITESLLVKMMNADMDTVDAENQ<MELEEKT*LINQVLHLQHTLEDLSARVDAVKEKNLKIK

Parental  SENQVLGQYIENLMSASSVFQTTDTKSKRK
          S.NQV..Q.IENLMS.SS.......K.K..
Retrocopy SDNQVIEQHIENLMSTSSFTNS*CKKQKKQ

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	111.58 RPM
SRP017611_kidney	0.00 RPM	63.29 RPM
SRP017611_liver	0.00 RPM	12.17 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_609 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_609 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010957	2 retrocopies	retro_amel_176, retro_amel_725,
Callithrix jacchus	ENSCJAG00000003060	2 retrocopies	retro_cjac_713, retro_cjac_95,
Erinaceus europaeus	ENSEEUG00000011107	1 retrocopy	retro_eeur_19,
Macropus eugenii	ENSMEUG00000014534	2 retrocopies	retro_meug_1580, retro_meug_823,
Monodelphis domestica	ENSMODG00000025528	2 retrocopies	retro_mdom_1163, retro_mdom_1265,
Mus musculus	ENSMUSG00000063253	2 retrocopies	retro_mmus_1639, retro_mmus_2306,
Oryctolagus cuniculus	ENSOCUG00000006591	3 retrocopies	retro_ocun_1400, retro_ocun_1657, retro_ocun_429,
Rattus norvegicus	ENSRNOG00000003853	1 retrocopy	retro_rnor_609 ,
Sarcophilus harrisii	ENSSHAG00000003474	1 retrocopy	retro_shar_572,
Tarsius syrichta	ENSTSYG00000011814	6 retrocopies	retro_tsyr_1232, retro_tsyr_1446, retro_tsyr_1566, retro_tsyr_2025, retro_tsyr_34, retro_tsyr_446,