RetrogeneDB ID: retro_rnor_1095

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:23199054..23199572(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Chtop
• Ensembl ID: ENSRNOG00000012760
• Aliases: Chtop, Fop, SRAG
• Description: Friend of PRMT1 protein [Source:UniProtKB/Swiss-Prot;Acc:Q498T2]

Sequence

>retro_rnor_1095
ATGGCTGCACTGTCAGCACCGAACGTTGTGCTAAAAAGCACCACCAAGGTGTCTCTAAATGAGCACTTTACTAGTGTGCT
GAAGAACAAACAGCCATGCCAGTGAATATTTGGTCTGGGATGCAGCAGCAGCAGCTAGCCAGTGCCAGAAACAGAAGACT
GGTCCAGCAGGTGGAGAAGGAACGCTCTGTCCAGGCAGCATTAAAACTTAAGCAGAGCTTAAAGCAGCGCCAGGGTGAGA
GGACCATCGAGGCACGGTTAGATCGACCCATAGGTGCTCTGGTCAGGGGAGCAGTTGGAGGAAGTGCCCTGCCCATGATC
CAGAGAGGCTTACCCAGAGGAGTACTACATGGGGGATGTGCCACCAGAACCCTGCTTAGGGTTGGGATGATGCTCTGAGG
TCAAAACCTACTCCGAGGTGGACAACTCGTAGCTTCCCGAATAGGCTTAAGAAGAGGTGGTGTTCAAGGTCGTGGAGGTC
CTGGAAGAGAGGGCCTAGGGCGTGGAGTTATGGGTCGT

Alignment

ORF - retro_rnor_1095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.71 %
• Parental protein coverage: 70.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAQSAPKVVLKSTTKMSLNERFTNMLKNKQP-MPVNIWASMQQQQQLASARNRRLAQQMENRPSVQAAL
          MAA.SAP.VVLKSTTK.SLNE.FT..LKNKQP.MPVNIW..MQQQQ.LASARNRRL.QQ.E...SVQAAL
Retrocopy MAALSAPNVVLKSTTKVSLNEHFTSVLKNKQP<MPVNIWSGMQQQQ-LASARNRRLVQQVEKERSVQAAL

Parental  KLKQSLKQRLGKSNIQARLGRPIGALARGAIGGRSLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLL
          KLKQSLKQR.G...I.ARL.RPIGAL.RGA.GG..LP.IQRGLPRG.L.GG.ATRTLLR.GM.L.GQNLL
Retrocopy KLKQSLKQRQGERTIEARLDRPIGALVRGAVGGSALPMIQRGLPRGVLHGGCATRTLLRVGMML*GQNLL

Parental  RGGRAVAPRMGLRRGGVRGRGGPGRGGLGRGAMGR
          RGG..VA.R.GLRRGGV.GRGGPGR.GLGRG.MGR
Retrocopy RGGQLVASRIGLRRGGVQGRGGPGREGLGRGVMGR

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	76.07 RPM
SRP017611_kidney	0.00 RPM	50.73 RPM
SRP017611_liver	0.00 RPM	27.03 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1095 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1095 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1095 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013518	1 retrocopy	retro_chof_6,
Callithrix jacchus	ENSCJAG00000010383	3 retrocopies	retro_cjac_2059, retro_cjac_423, retro_cjac_431,
Dasypus novemcinctus	ENSDNOG00000004834	1 retrocopy	retro_dnov_1054,
Equus caballus	ENSECAG00000020889	1 retrocopy	retro_ecab_729,
Felis catus	ENSFCAG00000002740	1 retrocopy	retro_fcat_1925,
Loxodonta africana	ENSLAFG00000002658	3 retrocopies	retro_lafr_131, retro_lafr_282, retro_lafr_656,
Myotis lucifugus	ENSMLUG00000016098	2 retrocopies	retro_mluc_201, retro_mluc_247,
Mus musculus	ENSMUSG00000001017	2 retrocopies	retro_mmus_1693, retro_mmus_1852,
Rattus norvegicus	ENSRNOG00000012760	1 retrocopy	retro_rnor_1095 ,
Ictidomys tridecemlineatus	ENSSTOG00000000660	1 retrocopy	retro_itri_1169,
Tupaia belangeri	ENSTBEG00000012442	1 retrocopy	retro_tbel_293,
Vicugna pacos	ENSVPAG00000010259	1 retrocopy	retro_vpac_353,