RetrogeneDB ID: retro_rnor_727

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:4111817..4112251(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cnbp
• Ensembl ID: ENSRNOG00000010239
• Aliases: Cnbp, Cnbp1, Znf9
• Description: Cellular nucleic acid-binding protein [Source:UniProtKB/Swiss-Prot;Acc:P62634]

Sequence

>retro_rnor_727
CGGGGTCGTGGAATGAGAAGCCGCGGCAGAGGGTTCCACCTTGTTTCCTCATCGCTTTTCTGACATCCCTTACCGCTATG
ATGAGTCTGGTCGTCTTGCCAAGGATTGTGATCTTCAGGAGGATGCCTGCTATAACTGTGATAGAGGCAGCCACATTGCC
AAGCACTGCAAGGAGCCCGAGAGAGGTGAGAGGCATGCAACTGCAACTATGGCAAGCCAGGCCATCTGGCTCAGAGTGTG
ACCACGCCGATGAGCAGAAGTGTTATTCTTGTGATGAACTTGGACATATTCAAAAAGACTGCACCAAGGTGAAGTGCTAT
AGGTGTGGTGAAACTGGTCATGTAGCCATCCGTTGCAGCAAGACAAGTGACGTCAGCTGTTAGCGCTGTGGTGAGTCAGG
GCATCTCTCACGGGAATGCACGATTGAGGGTACA

Alignment

ORF - retro_rnor_727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.35 %
• Parental protein coverage: 81.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RGRGGFTSDRGFQFVSSSL-PDICYRCGESGHLAKDCDLQEDACYNCGRGGHIAKDCKEPKRER-EQCCY
          RGRG.....RGF..VSSSL..DI.YR..ESG.LAKDCDLQEDACYNC.RG.HIAK.CKEP.R...E.C..
Retrocopy RGRGMRSRGRGFHLVSSSL>SDIPYRYDESGRLAKDCDLQEDACYNCDRGSHIAKHCKEPERGE<EACNC

Parental  NCGKPGHLAR-DCDHADEQKCYSCGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLA
          N.GKPGHLA...CDHADEQKCYSC.E.GHIQKDCTKVKCYRCGETGHVAI.CSKTS.V.C.RCGESGHL.
Retrocopy NYGKPGHLAQ<ECDHADEQKCYSCDELGHIQKDCTKVKCYRCGETGHVAIRCSKTSDVSC*RCGESGHLS

Parental  RECTIEAT
          RECTIE.T
Retrocopy RECTIEGT

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	185.56 RPM
SRP017611_kidney	0.21 RPM	199.51 RPM
SRP017611_liver	0.13 RPM	176.23 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_727 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_727 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015334	2 retrocopies	retro_amel_1285, retro_amel_1773,
Canis familiaris	ENSCAFG00000004320	2 retrocopies	retro_cfam_1272, retro_cfam_23,
Cavia porcellus	ENSCPOG00000012816	2 retrocopies	retro_cpor_424, retro_cpor_94,
Dipodomys ordii	ENSDORG00000002919	1 retrocopy	retro_dord_569,
Echinops telfairi	ENSETEG00000008408	5 retrocopies	retro_etel_12, retro_etel_1791, retro_etel_2192, retro_etel_237, retro_etel_583,
Felis catus	ENSFCAG00000028042	2 retrocopies	retro_fcat_1922, retro_fcat_2001,
Homo sapiens	ENSG00000169714	1 retrocopy	retro_hsap_50,
Gorilla gorilla	ENSGGOG00000010085	1 retrocopy	retro_ggor_2926,
Macropus eugenii	ENSMEUG00000011699	1 retrocopy	retro_meug_55,
Myotis lucifugus	ENSMLUG00000012554	1 retrocopy	retro_mluc_141,
Macaca mulatta	ENSMMUG00000011585	1 retrocopy	retro_mmul_2505,
Mustela putorius furo	ENSMPUG00000017315	3 retrocopies	retro_mputfur_1465, retro_mputfur_1555, retro_mputfur_583,
Mus musculus	ENSMUSG00000030057	1 retrocopy	retro_mmus_230,
Nomascus leucogenys	ENSNLEG00000014482	1 retrocopy	retro_nleu_1986,
Otolemur garnettii	ENSOGAG00000013898	1 retrocopy	retro_ogar_144,
Ochotona princeps	ENSOPRG00000005487	5 retrocopies	retro_opri_139, retro_opri_49, retro_opri_496, retro_opri_566, retro_opri_965,
Pongo abelii	ENSPPYG00000013423	1 retrocopy	retro_pabe_3658,
Pan troglodytes	ENSPTRG00000015369	1 retrocopy	retro_ptro_3131,
Rattus norvegicus	ENSRNOG00000010239	2 retrocopies	retro_rnor_207, retro_rnor_727 ,
Ictidomys tridecemlineatus	ENSSTOG00000000173	1 retrocopy	retro_itri_113,
Tarsius syrichta	ENSTSYG00000004344	1 retrocopy	retro_tsyr_1889,
Vicugna pacos	ENSVPAG00000007138	1 retrocopy	retro_vpac_548,