RetrogeneDB ID: retro_rnor_2952

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:86396051..86396381(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tusc2
• Ensembl ID: ENSRNOG00000021528
• Aliases: None
• Description: tumor suppressor candidate 2 [Source:RefSeq peptide;Acc:NP_001102767]

Sequence

>retro_rnor_2952
ATGGGCTCCAGCATCTCAAAAGCTCGGGGCTTGTGTCCCTTTGTGTCCACTACAGGGGTCGGCAGCCCAGTGGCTGAAGT
GGCTAAGCAATCTTTGGTGCGGTCTCGAGCCCGAGCAGTGCCTCCCTTCGTATTCACCCGCCGCGGCTCCATGTTCTATG
ATGAAGATGGGGATCTGGCTCACGAATTCTATGAGGAGACAATCATCACCAAGAATGGGCAGAAGCGATCCAACCTGAGG
CGAGTACGTAATAATCTGATTCCTCAGGGCATCGTGAAGCTGGAACGCCCACAAATCCACGTGGATTTCCCTCTGATCCT
CTGTGAAGTA

Alignment

ORF - retro_rnor_2952 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGASGSKARGLWPFASTTGGGGPEAAGAEQSLVRSRARAVPPFVFTRRGSMFYDEDGDLAHEFYEETIVT
          MG.S.SKARGL.PF.STTG.G.P.A..A.QSLVRSRARAVPPFVFTRRGSMFYDEDGDLAHEFYEETI.T
Retrocopy MGSSISKARGLCPFVSTTGVGSPVAEVAKQSLVRSRARAVPPFVFTRRGSMFYDEDGDLAHEFYEETIIT

Parental  KNGQKRAKLRRVHKNLIPQGIVKLDPPRIHVDFPVILYEV
          KNGQKR..LRRV..NLIPQGIVKL..P.IHVDFP.IL.EV
Retrocopy KNGQKRSNLRRVRNNLIPQGIVKLERPQIHVDFPLILCEV

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	45.58 RPM
SRP017611_kidney	0.00 RPM	27.56 RPM
SRP017611_liver	0.00 RPM	8.34 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2952 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2952 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000007859	2 retrocopies	retro_dord_20, retro_dord_590,
Mus musculus	ENSMUSG00000010054	2 retrocopies	retro_mmus_2347, retro_mmus_2349,
Oryctolagus cuniculus	ENSOCUG00000005259	1 retrocopy	retro_ocun_1687,
Rattus norvegicus	ENSRNOG00000021528	1 retrocopy	retro_rnor_2952 ,