RetrogeneDB ID: retro_rnor_2693

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:67607893..67608309(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psma7
• Ensembl ID: ENSRNOG00000008630
• Aliases: None
• Description: proteasome subunit alpha type-7 [Source:RefSeq peptide;Acc:NP_001008218]

Sequence

>retro_rnor_2693
CAAAGCCACTGACTGATCGTGGAGGACCCAGTGACTGTGGAGTACATCACCCACTACATTGCCAGTCTGAAGCAGCATTA
TACACAGAGCAATGGGTGCAGGACATTTGGTATCTCTGCCCTAATTGTGGGTTTTGACTTTGATGGCACCCTCAGACTCT
ATCAGACTGACCCCTTGGGCACATACTATGCTTGCAAGGCAAATGCCATAGGCTGGGGCACCAAGCTGGTGCATGAATTT
CTAAAGAAGAACTACACTGATGATGTCATCAAAACAAAGGAGCTGACCATCATCTAGTAATCAAGGCGTTGCTGGAAGTG
GTCCAGTCAGGTGACAGAAACATTGAACTTGCTGTCATGAGGCAGGATCAGCTCCTCAAGATTCTAGATCCTGAAGAAAT
TGAGAAGTATGTTGCT

Alignment

ORF - retro_rnor_2693 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.43 %
• Parental protein coverage: 54.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAI
          QSH.L.VEDPVTVEYIT.YIASLKQ.YTQSNG.R.FGISALIVGFDFDGT.RLYQTDP.GTY.A.KANAI
Retrocopy QSH*LIVEDPVTVEYITHYIASLKQHYTQSNGCRTFGISALIVGFDFDGTLRLYQTDPLGTYYACKANAI

Parental  GRGAKSVREFLEKNYTDDAIETDDLTI-KLVIKALLEVVQSGGKNIELAVMRRDQPLKILSPEEIEKYVA
          G.G.K.V.EFL.KNYTDD.I.T..LTI..LVIKALLEVVQSG..NIELAVMR.DQ.LKIL.PEEIEKYVA
Retrocopy GWGTKLVHEFLKKNYTDDVIKTKELTI<HLVIKALLEVVQSGDRNIELAVMRQDQLLKILDPEEIEKYVA

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	58.52 RPM
SRP017611_kidney	0.00 RPM	94.49 RPM
SRP017611_liver	0.00 RPM	55.94 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2693 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2693 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2693 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014419	1 retrocopy	retro_cjac_426,
Felis catus	ENSFCAG00000003249	1 retrocopy	retro_fcat_1621,
Mus musculus	ENSMUSG00000027566	1 retrocopy	retro_mmus_407,
Rattus norvegicus	ENSRNOG00000008630	1 retrocopy	retro_rnor_2693 ,
Ictidomys tridecemlineatus	ENSSTOG00000012489	1 retrocopy	retro_itri_279,
Tupaia belangeri	ENSTBEG00000012281	2 retrocopies	retro_tbel_1048, retro_tbel_2392,
Drosophila melanogaster	FBgn0004066	1 retrocopy	retro_dmel_63,