RetrogeneDB ID: retro_rnor_812

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:72263855..72264386(+)
• Located in intron of: ENSRNOG00000002215

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kxd1
• Ensembl ID: ENSRNOG00000019971
• Aliases: None
• Description: KxDL motif-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5M853]

Sequence

>retro_rnor_812
ATGGACACCCCAGACTCAGCCTCAAGGGTCTTCTGTGGCCGCTTCCTCAGCCTGGTGAACACTGGTGACGTCAATGCCAT
AATTGTGGCCCAGAAGAACATGCTGGACCTCTTCGAGAAAACCAATGAGATGTTTCTGAACTTCAACAATCCGTCCTGCG
TGCGGCTGTAACAGATGAGTGAGAGCTTCATGCACCATAGCCGCACCTTGGTGGACATGAAACGGAGCCTGGACAGCATT
TTCTGCAGGATTAGGACACTGAAGGGGAAGCTGGTCGAGCAGTATCCAGAGGCCTTCAGCCACACCCCAGAGGGTTCACT
CCTAGAGGACAAAGATGAAGACCCTGTTCCGCCCAGTATTGCCACAACCATTGTCACCTCAGAGCAGAGCACAGGCTCCT
GTGACACCAGCCCTGACACTGCCTCTCCATCCTTCGGTCTTGGCTTTGAAGTCCTATCACACATGTGACCTGGCTCTCCT
GCCATCAACGGCCACAGCCAGACAGATGATGAGGAAGAGACACGTGAAGAA

Alignment

ORF - retro_rnor_812 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTPDSASRVFCGRFLSMVNTDDVNAIILAQKNMLDRFEKTNEMLLNFNNLSSVRLQQMSERFMHHTRTL
          MDTPDSASRVFCGRFLS.VNT.DVNAII.AQKNMLD.FEKTNEM.LNFNN.S.VRL.QMSE.FMHH.RTL
Retrocopy MDTPDSASRVFCGRFLSLVNTGDVNAIIVAQKNMLDLFEKTNEMFLNFNNPSCVRL*QMSESFMHHSRTL

Parental  VDMKRDLDSIFRRIRTLKGKLARQHPEAFSHIPEGSLLEDEDEDPVPPSITTTIATSEQSTGSCDTSPDT
          VDMKR.LDSIF.RIRTLKGKL..Q.PEAFSH.PEGSLLED.DEDPVPPSI.TTI.TSEQSTGSCDTSPDT
Retrocopy VDMKRSLDSIFCRIRTLKGKLVEQYPEAFSHTPEGSLLEDKDEDPVPPSIATTIVTSEQSTGSCDTSPDT

Parental  ASPSFSPGFEDLSHIRPGSPAINGHSQTDDEEETREE
          ASPSF..GFE.LSH..PGSPAINGHSQTDDEEETREE
Retrocopy ASPSFGLGFEVLSHM*PGSPAINGHSQTDDEEETREE

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	22.50 RPM
SRP017611_kidney	0.07 RPM	24.77 RPM
SRP017611_liver	0.07 RPM	36.58 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_812 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_812 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_812 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010545	1 retrocopy	retro_btau_689,
Echinops telfairi	ENSETEG00000003390	2 retrocopies	retro_etel_1213, retro_etel_2129,
Macropus eugenii	ENSMEUG00000013150	1 retrocopy	retro_meug_2148,
Monodelphis domestica	ENSMODG00000003489	1 retrocopy	retro_mdom_1623,
Mus musculus	ENSMUSG00000055553	6 retrocopies	retro_mmus_1117, retro_mmus_3557, retro_mmus_799, retro_mmus_800, retro_mmus_802, retro_mmus_804,
Rattus norvegicus	ENSRNOG00000019971	2 retrocopies	retro_rnor_2808, retro_rnor_812 ,