RetrogeneDB ID: retro_rnor_965

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:64245103..64245467(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rnf138
• Ensembl ID: ENSRNOG00000015645
• Aliases: None
• Description: E3 ubiquitin-protein ligase RNF138 [Source:RefSeq peptide;Acc:NP_446040]

Sequence

>retro_rnor_965
TGCTGTTCAAAAGATTCAATTTTATCACATGAGACATCATCACAAATCTTGTAAGAAATATCAAGATGAATATGGTGTTT
CTTCTGTAATTCCAAACTTTAAGATTTCTCAAGATTCAGTAAGGAGCAGTAATAGCAATGAAGTATCTTCATGTAATAAC
ACAGAAACTTATCAGGTGGATATAAGTTCTTCTGGGCATTCCACCTTTAAGTGTCCCTCATGTCAAGAGTCAAATATCAC
TAGACAAAGTTTATTGGATCACTTTAATAGTAACCACCTATTTCAGATAATTTTTGAGAATCTTCAGCTAGGTGAGGAAA
CCCAATACCAAACTGCTGTGGAAGGGTCTTTTTAAGTAAACATG

Alignment

ORF - retro_rnor_965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.51 %
• Parental protein coverage: 69.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CCIK-IKFYRMRHHYKSCKKYQDEYGVSSVIPNVKISQDSVRSSNRSETSASDNTETYQEDTSSSGHPTF
          CC.K.I.FY.MRHH.KSCKKYQDEYGVSSVIPN.KISQDSVRSSN..E.S...NTETYQ.D.SSSGH.TF
Retrocopy CCSK>IQFYHMRHHHKSCKKYQDEYGVSSVIPNFKISQDSVRSSNSNEVSSCNNTETYQVDISSSGHSTF

Parental  KCPLCQESNFTRQRLLDHCNSNHLFQIVPVNLQLDEETQYQTAVEESFQVNM
          KCP.CQESN.TRQ.LLDH.NSNHLFQI...NLQL.EETQYQTAVE.SF.VNM
Retrocopy KCPSCQESNITRQSLLDHFNSNHLFQIIFENLQLGEETQYQTAVEGSF*VNM

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	13.23 RPM
SRP017611_kidney	0.00 RPM	9.77 RPM
SRP017611_liver	0.00 RPM	5.92 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_965 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_965 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_965 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_494

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020160	1 retrocopy	retro_btau_322,
Choloepus hoffmanni	ENSCHOG00000012689	6 retrocopies	retro_chof_1043, retro_chof_1242, retro_chof_1931, retro_chof_418, retro_chof_714, retro_chof_793,
Callithrix jacchus	ENSCJAG00000020875	1 retrocopy	retro_cjac_2325,
Felis catus	ENSFCAG00000014180	2 retrocopies	retro_fcat_1383, retro_fcat_379,
Homo sapiens	ENSG00000134758	1 retrocopy	retro_hsap_3319,
Gorilla gorilla	ENSGGOG00000027857	1 retrocopy	retro_ggor_1302,
Loxodonta africana	ENSLAFG00000003811	1 retrocopy	retro_lafr_408,
Monodelphis domestica	ENSMODG00000010850	4 retrocopies	retro_mdom_1468, retro_mdom_387, retro_mdom_708, retro_mdom_725,
Mustela putorius furo	ENSMPUG00000006982	1 retrocopy	retro_mputfur_276,
Nomascus leucogenys	ENSNLEG00000006401	1 retrocopy	retro_nleu_1665,
Pongo abelii	ENSPPYG00000009094	1 retrocopy	retro_pabe_2734,
Pan troglodytes	ENSPTRG00000009956	1 retrocopy	retro_ptro_2155,
Pteropus vampyrus	ENSPVAG00000003778	2 retrocopies	retro_pvam_1316, retro_pvam_1379,
Rattus norvegicus	ENSRNOG00000015645	3 retrocopies	retro_rnor_2316, retro_rnor_808, retro_rnor_965 ,
Ictidomys tridecemlineatus	ENSSTOG00000002293	2 retrocopies	retro_itri_1443, retro_itri_576,