RetrogeneDB ID: retro_rnor_1111

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:55658948..55659270(+)
• Located in intron of: ENSRNOG00000009745

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mpc1
• Ensembl ID: ENSRNOG00000012415
• Aliases: Mpc1, Brp44l
• Description: Mitochondrial pyruvate carrier 1 [Source:UniProtKB/Swiss-Prot;Acc:P63031]

Sequence

>retro_rnor_1111
GCTGGAGCACCGGTGTGCAAAGCGGCAGACTATGACCAAGCAAGGACTTCCAGGACTATCTCATGAGTATGAACTTCTGG
GGACCAGTTGCCAACTGGGGTCTCCCCACTGCTGCTATCAATGACATGAAGAACTCTCCACAGATTATCAGTGAGCAGAT
GACTTTTGCCCTCTGTTGCTATTCTCAACATTCACAAGATTTGCCTACAAGGTACAACCTTGAAACTGGCTTCTGTTTAC
GTGCCATGTGACAAACGAAGTAGCTCAGCTCATTCAGGGAGGACGACTTATCAACTACGAGATGAGTAAGTGGCCATCTG
CG

Alignment

ORF - retro_rnor_1111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.73 %
• Parental protein coverage: 99.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGALVRKAADYVR-SKDFRDYLMSTHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALCCYS-LTFMRF
          AGA.V.KAADY...SKDF.DYLMS..FWGPVANWGLP.AAINDMK.SP.IIS..MTFALCCYS..TF.RF
Retrocopy AGAPVCKAADYDQ<SKDFQDYLMSMNFWGPVANWGLPTAAINDMKNSPQIISEQMTFALCCYS<STFTRF

Parental  AYKVQPRNWLLFACHVTNEVAQLIQGGRLINYEMSKRPSA
          AYKVQP.NWLLF.CHVTNEVAQLIQGGRLINYEMSK.PSA
Retrocopy AYKVQP*NWLLFTCHVTNEVAQLIQGGRLINYEMSKWPSA

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	58.60 RPM
SRP017611_kidney	0.00 RPM	259.17 RPM
SRP017611_liver	0.00 RPM	133.53 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1111 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1111 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027879	1 retrocopy	retro_btau_43,
Callithrix jacchus	ENSCJAG00000012552	2 retrocopies	retro_cjac_2102, retro_cjac_4053,
Dasypus novemcinctus	ENSDNOG00000001205	1 retrocopy	retro_dnov_2139,
Homo sapiens	ENSG00000060762	1 retrocopy	retro_hsap_4675,
Myotis lucifugus	ENSMLUG00000000583	1 retrocopy	retro_mluc_28,
Mus musculus	ENSMUSG00000023861	3 retrocopies	retro_mmus_2037, retro_mmus_3420, retro_mmus_979,
Ornithorhynchus anatinus	ENSOANG00000004153	1 retrocopy	retro_oana_45,
Pongo abelii	ENSPPYG00000017166	1 retrocopy	retro_pabe_17,
Rattus norvegicus	ENSRNOG00000012415	3 retrocopies	retro_rnor_1111 , retro_rnor_2632, retro_rnor_296,
Tursiops truncatus	ENSTTRG00000004456	1 retrocopy	retro_ttru_663,