RetrogeneDB ID: retro_rnor_2231

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:94100328..94100637(-)
• Located in intron of: ENSRNOG00000006503

Retrocopy information

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

Parental gene information

• Parental gene symbol: Commd2
• Ensembl ID: ENSRNOG00000043386
• Aliases: None
• Description: COMM domain-containing protein 2 [Source:RefSeq peptide;Acc:NP_001102973]

Sequence

>retro_rnor_2231
ATGCTGCTGGATTTGTTCGAGGAGCACCTGGCCTTCCTGCCACAAGTGGAGAGCACGGTGGTCGCCAAGTTCGGAAGATC
GCCTTGGAGTTCCTCAGACAGGGATCAAACCCGAAGATCTATGAAGGCGCCACCAGAAATCTTAGTGTGAGTAGTGGCAC
TATCCATCATGGTGTGGAAGGATTAACATATCTCCTCACCGAGAGCTCAAAGCTCATGACTTCTGAACTGGATTTCAAAT
TCTGTTTTTATTCTGGGATTCTCTGAAGAATCGAACAAATTATTGCTTCAGCTCTACCTGGACAACAAA

Alignment

ORF - retro_rnor_2231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 53.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLLDLSEEHKEHLAFLPQVDSAVVAEFGR-IAVEFLRRGSNPKIYEGAARKLNVSSDTIQHGVEGLTYLL
          MLLDL.E...EHLAFLPQV.S.VVA.FGR.IA.EFLR.GSNPKIYEGA.R.L.VSS.TI.HGVEGLTYLL
Retrocopy MLLDLFE---EHLAFLPQVESTVVAKFGR<IALEFLRQGSNPKIYEGATRNLSVSSGTIHHGVEGLTYLL

Parental  TESSKLMISELD-FQ-DSVFVLGFSEELNKLLLQLYLDNR
          TESSKLM.SELD.FQ..SVF.LGFSEE.NKLLLQLYLDN.
Retrocopy TESSKLMTSELD<FQ<NSVFILGFSEESNKLLLQLYLDNK

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	7.69 RPM
SRP017611_kidney	0.00 RPM	10.82 RPM
SRP017611_liver	0.00 RPM	6.79 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2231 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2231 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2231 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013809	1 retrocopy	retro_chof_1601,
Cavia porcellus	ENSCPOG00000005273	2 retrocopies	retro_cpor_520, retro_cpor_956,
Rattus norvegicus	ENSRNOG00000043386	1 retrocopy	retro_rnor_2231 ,
Ictidomys tridecemlineatus	ENSSTOG00000010888	4 retrocopies	retro_itri_180, retro_itri_1803, retro_itri_1880, retro_itri_1899,
Tupaia belangeri	ENSTBEG00000003545	1 retrocopy	retro_tbel_2895,
Tursiops truncatus	ENSTTRG00000003450	1 retrocopy	retro_ttru_1759,