RetrogeneDB ID: retro_rnor_1239

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:74279072..74279319(-)
• Located in intron of: ENSRNOG00000024837

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hmgn1
• Ensembl ID: ENSRNOG00000048226
• Aliases: None
• Description: high-mobility group nucleosome binding domain 1 [Source:RefSeq peptide;Acc:NP_001013202]

Sequence

>retro_rnor_1239
GGAGCTCTGAAGGTGGAGCCCAAGAGCTGCTCCGTGAGCCTGTAGGCTAAGCCCGCCCCTGCCAAGGCAGATGCAAAGCC
GAAAAAAAGTCTCAGGAAAGGATAAATGATCAGACAAAAAAGTGCAGACAAAAGGGACGTGGGGAGCAAAGGGCAGACAG
GTTGAAGTGGTTGACCAGCAAAACACACATCTGCCTTCAGAAAATGGAGACGGAAAACCAGAGTCCAATCTCCGGAAAAG
AGAAAGA

Alignment

ORF - retro_rnor_1239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.24 %
• Parental protein coverage: 85.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAAKAEPKRRSARLSAKPAPAKVDAKPKKA-AGKDKASDKKAQIKGKRGAKGKQAEVADQQTTDLPAENG
          GA.K.EPK..S..L.AKPAPAK.DAKPKK...GKDK.SDKK.Q.KG..GAKG.Q.EV.DQQ.T.LP.ENG
Retrocopy GALKVEPKSCSVSL*AKPAPAKADAKPKKS>SGKDK*SDKKVQTKGTWGAKGRQVEVVDQQNTHLPSENG

Parental  ETENQSPASEEEK
          .....S.....E.
Retrocopy DGKPESNLRKRER

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	0.07 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1239 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1239 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1239 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_3117

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002336	7 retrocopies	retro_cpor_1129, retro_cpor_1389, retro_cpor_334, retro_cpor_349, retro_cpor_4, retro_cpor_884, retro_cpor_949,
Monodelphis domestica	ENSMODG00000020972	5 retrocopies	retro_mdom_1085, retro_mdom_109, retro_mdom_284, retro_mdom_755, retro_mdom_88,
Mustela putorius furo	ENSMPUG00000008550	3 retrocopies	retro_mputfur_252, retro_mputfur_371, retro_mputfur_483,
Mus musculus	ENSMUSG00000040681	13 retrocopies	retro_mmus_1274, retro_mmus_1295, retro_mmus_1445, retro_mmus_1565, retro_mmus_1574, retro_mmus_1636, retro_mmus_2166, retro_mmus_2195, retro_mmus_2895, retro_mmus_3117, retro_mmus_3641, retro_mmus_832, retro_mmus_949,
Rattus norvegicus	ENSRNOG00000048226	8 retrocopies	retro_rnor_1020, retro_rnor_1239 , retro_rnor_1290, retro_rnor_2643, retro_rnor_2667, retro_rnor_642, retro_rnor_764, retro_rnor_966,
Rattus norvegicus	ENSRNOG00000050978	5 retrocopies	retro_rnor_1057, retro_rnor_1318, retro_rnor_1389, retro_rnor_2433, retro_rnor_358,