RetrogeneDB ID: retro_rnor_1464

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:56733384..56733858(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdc34
• Ensembl ID: ENSRNOG00000008348
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 R1 [Source:RefSeq peptide;Acc:NP_001013121]

Sequence

>retro_rnor_1464
CACCCATATTCCCCACAAGCCTTCCGGTTCCTCACCAAGACGTGGCACCCAAACATCTATGAGTCAGGGGACGTGTGCAT
CTCCATCCTCCACCCCCAAGTTGACGACCCACAGAGTGGGGAGCTGCCCTCAGAGCGGTGGAACCCCACGCAGAATGTCA
GGACCATCCTCCTGAGTGTGATCTCCCTGCGGAATGAGCCCAACAACTTCTTGCCTGCCGACGTGGACGCCTCGGAGACA
TACAGAAAATGGAAAGAGAGCAAGGGGAAGGACTGCGAGTACACGGACATCATCCGGAAGCAGGTTCTGGGGACCAAGGT
GGACGCAGAGCGCGATGGCGTGAAGGTGCCCACCACGCTGGCTGAGGTCTGCGTGAAGACCAAGGCGCTGGTGCCAGACG
AGGGTTCAGACCTCTTCTAAGACTATGAGGACAGCGAAGTGGAGGAGGCCGACAGCTGCTTTGGGGATGAAGAG

Alignment

ORF - retro_rnor_1464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.12 %
• Parental protein coverage: 68.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPYSPPAFRFLTKMWHPNIYETGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTF
          .PYSP.AFRFLTK.WHPNIYE.GDVCISILHP.VDDPQSGELPSERWNPTQNVRTILLSVISL.NEPN.F
Retrocopy HPYSPQAFRFLTKTWHPNIYESGDVCISILHPQVDDPQSGELPSERWNPTQNVRTILLSVISLRNEPNNF

Parental  SPANVDASVMYRKWKESKGKDREYTDIIRKQVLGTKVDAERDGVKVPTTLAEYCVKTKAPAPDEGSDLFY
          .PA.VDAS..YRKWKESKGKD.EYTDIIRKQVLGTKVDAERDGVKVPTTLAE.CVKTKA..PDEGSDLF.
Retrocopy LPADVDASETYRKWKESKGKDCEYTDIIRKQVLGTKVDAERDGVKVPTTLAEVCVKTKALVPDEGSDLF*

Parental  DDYYEDGEVEEADSCFGDEE
          D..YED.EVEEADSCFGDEE
Retrocopy D--YEDSEVEEADSCFGDEE

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	34.15 RPM
SRP017611_kidney	0.00 RPM	23.31 RPM
SRP017611_liver	0.00 RPM	15.73 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1464 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1464 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000023874	1 retrocopy	retro_cpor_743,
Macropus eugenii	ENSMEUG00000000812	1 retrocopy	retro_meug_1683,
Mus musculus	ENSMUSG00000020307	1 retrocopy	retro_mmus_23,
Ochotona princeps	ENSOPRG00000001017	1 retrocopy	retro_opri_464,
Rattus norvegicus	ENSRNOG00000008348	1 retrocopy	retro_rnor_1464 ,
Rattus norvegicus	ENSRNOG00000010041	3 retrocopies	retro_rnor_2496, retro_rnor_317, retro_rnor_970,
Rattus norvegicus	ENSRNOG00000010727	1 retrocopy	retro_rnor_1508,
Ictidomys tridecemlineatus	ENSSTOG00000023255	1 retrocopy	retro_itri_822,
Tursiops truncatus	ENSTTRG00000000391	2 retrocopies	retro_ttru_1142, retro_ttru_98,