RetrogeneDB ID: retro_rnor_1955

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:22094446..22094755(+)
• Located in intron of: ENSRNOG00000029207

Retrocopy information

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

Parental gene information

• Parental gene symbol: 1810009A15Rik
• Ensembl ID: ENSRNOG00000019701
• Aliases: LOC690349, RGD1304652
• Description: RIKEN cDNA 1810009A15 gene [Source:MGI Symbol;Acc:MGI:1913526]

Sequence

>retro_rnor_1955
GAGCTGAAAAAGAAGTTGTTCAAGTACGGCAGGGAACTAAGCAGGGATCATCAACGGAAGCACCAGGTGGTCGGGGCTGT
GATAGACAGAGGGCTGACGAGGAGACACCACCTCAGGAAGCGTGCATGCAGTTCGTGTGCCAACATCATGCTATTTGGGA
AGCACGGGAAACTCTTGCCCAGAAAGAAAAAGCAGCCATGGAAGTGGAAGTTCCCTCCAAGTCAACCAGGACTAGTCAGC
CATAGCCCAAAAGATAAAAGAAGATAAAAAGCTCCCCAGGACGTAGATATGGAAGATCTTGGAGATAAA

Alignment

ORF - retro_rnor_1955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.36 %
• Parental protein coverage: 88.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELKKKLFKRRRVLSRDRRRKRLVVGAVIDEGLTTKHHLKKRASSARANITLSGK-KRRKLLQQIRLAQKE
          ELKKKLFK..R.LSRD..RK..VVGAVID.GLT..HHL.KRA.S..ANI.L.GK..R..L.Q....A...
Retrocopy ELKKKLFKYGRELSRDHQRKHQVVGAVIDRGLTRRHHLRKRACSSCANIMLFGK<ARETLAQKEKAAME-

Parental  KAAMEVEVLSTSTGTSQPKPKRQKKT-QAPQDVDMEDLEDK
          ....EV...ST.T..SQP.PKR.KK...APQDVDMEDL.DK
Retrocopy ---VEVPSKSTRT--SQP*PKR*KKI>KAPQDVDMEDLGDK

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	0.14 RPM	5.25 RPM
SRP017611_kidney	0.07 RPM	10.26 RPM
SRP017611_liver	0.47 RPM	6.32 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1955 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1955 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1955 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006512	1 retrocopy	retro_amel_1386,
Bos taurus	ENSBTAG00000010465	2 retrocopies	retro_btau_1195, retro_btau_1799,
Canis familiaris	ENSCAFG00000015719	2 retrocopies	retro_cfam_1104, retro_cfam_757,
Felis catus	ENSFCAG00000025454	2 retrocopies	retro_fcat_1722, retro_fcat_773,
Macaca mulatta	ENSMMUG00000013949	4 retrocopies	retro_mmul_1186, retro_mmul_1541, retro_mmul_1785, retro_mmul_1981,
Mus musculus	ENSMUSG00000071653	2 retrocopies	retro_mmus_1809, retro_mmus_759,
Otolemur garnettii	ENSOGAG00000033103	1 retrocopy	retro_ogar_811,
Rattus norvegicus	ENSRNOG00000019701	4 retrocopies	retro_rnor_1066, retro_rnor_1955 , retro_rnor_851, retro_rnor_883,
Sus scrofa	ENSSSCG00000023323	2 retrocopies	retro_sscr_1162, retro_sscr_1163,