RetrogeneDB ID: retro_rnor_1582

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:253425730..253426259(+)
• Located in intron of: ENSRNOG00000047744

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psmb7
• Ensembl ID: ENSRNOG00000011732
• Aliases: None
• Description: Proteasome subunit beta type-7 [Source:UniProtKB/Swiss-Prot;Acc:Q9JHW0]

Sequence

>retro_rnor_1582
ACCCAGCTTATTTCTTCTAACTTGGAGCTCCACTTTCTCACCACTGGCCGCCTTCAGAGAGTTGTTACAGAGAATGGGAT
GCTGAAGCAGATGCTTTTCAGGTATCACAATTACATGGTGCAGCCCTAGTTTTGGGGGTAGTAGACAGTACTGGACCTCA
TCTCTACAGCACCTGTCCTCATGGATCAACTGATAAATTGCTTATGTCACCATGGGTTCTGGCTCCTTGGCAGCAATGGC
TGCTTTTGAAGATAAGTTTAGGCCAGATATGGAGGAGGACAAAGCCAAGAAGCTAGTGAGCGAGGCATTGCAGCTGGCAT
CTTTAATGACTTGGGGTCTGGAAGCAATATTGATCTGTGTGTTACCAGCAAGGGCAAGCTGGACTTCTCTCCATCCATAC
TCAGTGCCCAACAAGAAAGGGACCAGGCTTGGCCGGTACAGGTGTGAGAAAGGCACTACCGCTGTCCTCTCCGAGAAAGT
CACCCCTCTGGAGTTCGAGGTGCTAGAAGAGACTGTTCAGACAATGGAC

Alignment

ORF - retro_rnor_1582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.64 %
• Parental protein coverage: 63.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TQLISSNLELHSLTTGRLPRVVTANRMLKQMLFRYQGYI-GAALVLGGVDVTGPHLYSIYPHGSTDKL-P
          TQLISSNLELH.LTTGRL.RVVT.N.MLKQMLFRY..Y..GAALVLG.VD.TGPHLYS..PHGSTDKL..
Retrocopy TQLISSNLELHFLTTGRLQRVVTENGMLKQMLFRYHNYM<GAALVLGVVDSTGPHLYSTCPHGSTDKL<A

Parental  YVTMGSGSLAAMAVFEDKFRPDMEEEEAKKLVSEA-IAAGIFNDLGSGSNIDLCVISKSKLDF-LRPYSV
          YVTMGSGSLAAMA.FEDKFRPDMEE..AKKLVSEA.IAAGIFNDLGSGSNIDLCV.SK.KLDF.L.PYSV
Retrocopy YVTMGSGSLAAMAAFEDKFRPDMEEDKAKKLVSEA<IAAGIFNDLGSGSNIDLCVTSKGKLDF>LHPYSV

Parental  PNKKGTRFGRYRCEKGTTAVLTEKVTPLELEVLEEIVQTMD
          PNKKGTR.GRYRCEKGTTAVL.EKVTPLE.EVLEE.VQTMD
Retrocopy PNKKGTRLGRYRCEKGTTAVLSEKVTPLEFEVLEETVQTMD

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	66.86 RPM
SRP017611_kidney	0.00 RPM	60.99 RPM
SRP017611_liver	0.00 RPM	50.76 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1582 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1582 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1582 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003067	2 retrocopies	retro_btau_1722, retro_btau_983,
Echinops telfairi	ENSETEG00000005432	2 retrocopies	retro_etel_2093, retro_etel_231,
Homo sapiens	ENSG00000136930	1 retrocopy	retro_hsap_1303,
Gorilla gorilla	ENSGGOG00000012164	1 retrocopy	retro_ggor_1019,
Nomascus leucogenys	ENSNLEG00000017268	1 retrocopy	retro_nleu_2947,
Otolemur garnettii	ENSOGAG00000003513	1 retrocopy	retro_ogar_2828,
Pongo abelii	ENSPPYG00000019596	1 retrocopy	retro_pabe_1092,
Pan troglodytes	ENSPTRG00000021354	1 retrocopy	retro_ptro_893,
Pteropus vampyrus	ENSPVAG00000000204	2 retrocopies	retro_pvam_1271, retro_pvam_866,
Rattus norvegicus	ENSRNOG00000011732	3 retrocopies	retro_rnor_1581, retro_rnor_1582 , retro_rnor_2469,
Sorex araneus	ENSSARG00000009395	1 retrocopy	retro_sara_532,
Tupaia belangeri	ENSTBEG00000009196	2 retrocopies	retro_tbel_2889, retro_tbel_751,