RetrogeneDB ID: retro_rnor_2804

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:55825140..55825746(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psmb3
• Ensembl ID: ENSRNOG00000012938
• Aliases: None
• Description: proteasome subunit beta type-3 [Source:RefSeq peptide;Acc:NP_058981]

Sequence

>retro_rnor_2804
ATGTCTATTATGTGCTATAATGGAGGGGCCATGACGGCTATGAAGGGAAAGAACTGTGTGGCCATCGCTGCAGACAGGCG
TTTCGGAATCCAGGCCCAAATGGTGACCACGGACTTCCAGAAGATCTTTCCCATGGGTGACAGGCTCTACATAGGCCTGG
CCGGTCTGGCCACTGATGTCCAGACAGTTGTCCAGCGTCTCAAGTTCCGACTGAACCTGTATGAGCTGAAGTAAGGACGG
CAGATCAAGCCTTACACCCTCTTGAGCATGGTGGCCAACCTCTTGTAGGAGAAACAGTTTGGTCCATACTACACAGAACC
TATCATTGCTGGCTTGGACCCGAAGACCTTTAAGCCCTTCATTTGCTCTCTGGGCCTCATTGGCTGTTCCATGGTGACCG
ATGACTTCATAGTCAGTGGCACCTGCTCTGAACAAATGTATGGGATGTGCGAGTCTCTCTGGGAGCCCAACATGGATCCA
GAACACCTGTTTGAAACCATTTCTCAGGCCATGCTGAATGCTGTGGACCGGGATGCCATGTCCGGTATGGGCGTCATTGT
CCACATCATTGAAAAAGACAAGATCACCACCAGGACACTGAAGGCC

Alignment

ORF - retro_rnor_2804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.58 %
• Parental protein coverage: 98.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFR
          MS.M.YNGGA..AMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTV.QRLKFR
Retrocopy MSIMCYNGGAMTAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTVVQRLKFR

Parental  LNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSG
          LNLYELK.GRQIKPYTL.SMVANLL.EK.FGPYYTEP.IAGLDPKTFKPFICSL.LIGC.MVTDDF.VSG
Retrocopy LNLYELK*GRQIKPYTLLSMVANLL*EKQFGPYYTEPIIAGLDPKTFKPFICSLGLIGCSMVTDDFIVSG

Parental  TCSEQMYGMCESLWEPNMEPEHLFETISTPMLNAVDRDAVSGMGVIVHIIEKDKITTRTLKA
          TCSEQMYGMCESLWEPNM.PEHLFETIS..MLNAVDRDA.SGMGVIVHIIEKDKITTRTLKA
Retrocopy TCSEQMYGMCESLWEPNMDPEHLFETISQAMLNAVDRDAMSGMGVIVHIIEKDKITTRTLKA

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	2.88 RPM	28.61 RPM
SRP017611_kidney	3.49 RPM	34.61 RPM
SRP017611_liver	3.09 RPM	30.19 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2804 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2804 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2804 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004363	1 retrocopy	retro_amel_619,
Canis familiaris	ENSCAFG00000016587	2 retrocopies	retro_cfam_135, retro_cfam_532,
Callithrix jacchus	ENSCJAG00000008246	1 retrocopy	retro_cjac_2852,
Equus caballus	ENSECAG00000000987	1 retrocopy	retro_ecab_476,
Erinaceus europaeus	ENSEEUG00000015275	1 retrocopy	retro_eeur_10,
Felis catus	ENSFCAG00000014497	3 retrocopies	retro_fcat_1270, retro_fcat_1442, retro_fcat_784,
Homo sapiens	ENSG00000108294	2 retrocopies	retro_hsap_1121, retro_hsap_2387,
Gorilla gorilla	ENSGGOG00000007067	2 retrocopies	retro_ggor_103, retro_ggor_876,
Loxodonta africana	ENSLAFG00000002233	1 retrocopy	retro_lafr_70,
Macropus eugenii	ENSMEUG00000004131	2 retrocopies	retro_meug_1804, retro_meug_551,
Microcebus murinus	ENSMICG00000002997	1 retrocopy	retro_mmur_397,
Macaca mulatta	ENSMMUG00000012363	1 retrocopy	retro_mmul_868,
Monodelphis domestica	ENSMODG00000012614	2 retrocopies	retro_mdom_1722, retro_mdom_1812,
Mus musculus	ENSMUSG00000069744	8 retrocopies	retro_mmus_1449, retro_mmus_1551, retro_mmus_1790, retro_mmus_1938, retro_mmus_2110, retro_mmus_41, retro_mmus_46, retro_mmus_536,
Nomascus leucogenys	ENSNLEG00000000594	3 retrocopies	retro_nleu_1511, retro_nleu_188, retro_nleu_371,
Oryctolagus cuniculus	ENSOCUG00000002598	1 retrocopy	retro_ocun_561,
Pongo abelii	ENSPPYG00000008505	2 retrocopies	retro_pabe_2153, retro_pabe_927,
Pteropus vampyrus	ENSPVAG00000002270	1 retrocopy	retro_pvam_822,
Rattus norvegicus	ENSRNOG00000012938	7 retrocopies	retro_rnor_1016, retro_rnor_2094, retro_rnor_2448, retro_rnor_2537, retro_rnor_2804 , retro_rnor_743, retro_rnor_8,
Ictidomys tridecemlineatus	ENSSTOG00000014258	3 retrocopies	retro_itri_527, retro_itri_935, retro_itri_936,
Tupaia belangeri	ENSTBEG00000013010	2 retrocopies	retro_tbel_1387, retro_tbel_2693,