RetrogeneDB ID: retro_rnor_2012

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:219503873..219504119(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Commd6
• Ensembl ID: ENSRNOG00000038012
• Aliases: Commd6, RGD1560745
• Description: COMM domain-containing protein 6 [Source:RefSeq peptide;Acc:NP_001102575]

Sequence

>retro_rnor_2012
GTGTTTGCAATTTCCACTCTGGCCAAGGAGGAGTCTCAGTTCAGGGAGCCGGTGCTGGACGCCAAGTCAGATGTCACCGG
CCAGCTTATAGACTTTCAGTGGAAACTGGGCATGGCTGTGAGCTCCGACAGCTGCAGATCTCTCAGGTATCCTTAGGTGG
TGGTGATGCTGAAGGTGACAGATGATTCTGGCCAAGTAAGCAGTAAGTCCATGGAAATGACAATCCCACAGTTTCAGAAT
TTCCAC

Alignment

ORF - retro_rnor_2012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.93 %
• Parental protein coverage: 75.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLAISTLAMEGSQYREPVLDAKSEVTGQLVDFQWKLGMAVSSDSCRSLKYPYVAVLLKVADHSGQVSSKS
          V.AISTLA.E.SQ.REPVLDAKS.VTGQL.DFQWKLGMAVSSDSCRSL.YP.V.V.LKV.D.SGQVSSKS
Retrocopy VFAISTLAKEESQFREPVLDAKSDVTGQLIDFQWKLGMAVSSDSCRSLRYP*VVVMLKVTDDSGQVSSKS

Parental  IEMTIPQFQNFY
          .EMTIPQFQNF.
Retrocopy MEMTIPQFQNFH

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	5.90 RPM
SRP017611_kidney	0.00 RPM	6.56 RPM
SRP017611_liver	0.00 RPM	5.65 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2012 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2012 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011048	1 retrocopy	retro_dord_237,
Erinaceus europaeus	ENSEEUG00000006061	2 retrocopies	retro_eeur_120, retro_eeur_560,
Myotis lucifugus	ENSMLUG00000010697	1 retrocopy	retro_mluc_1927,
Monodelphis domestica	ENSMODG00000000970	3 retrocopies	retro_mdom_111, retro_mdom_147, retro_mdom_76,
Nomascus leucogenys	ENSNLEG00000026952	1 retrocopy	retro_nleu_2240,
Rattus norvegicus	ENSRNOG00000038012	1 retrocopy	retro_rnor_2012 ,
Tursiops truncatus	ENSTTRG00000003379	2 retrocopies	retro_ttru_1697, retro_ttru_908,