RetrogeneDB ID: retro_mmus_2887

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:3181092..3181885(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psmb5
• Ensembl ID: ENSMUSG00000022193
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type 5 [Source:MGI Symbol;Acc:MGI:1194513]

Sequence

>retro_mmus_2887
ATGGCACTGGCTAGCGTGTTGCAGCGGCCGATGCCGGTGAATCAGCACGGGTTTTTTGGGCTCGGAGGTGGTGCAGATCT
GCTGGACTTGGGTCCGGGGAGTCCTAGTGATGGGCTGAGCCTAGCCGCGCCGAGCTGGGGCGTCCCGGAGGAGCCGCGAA
TCGAAATGCTTCACGGAACCACCACCCTGGCCTTCAAGTTTCTCCATGGAGTCATTGTTGCAGCGGATTCCCGGGCCACA
GCAGGTGCTTATATTGCTTCCCAAGACGGTGAAGAAAGTAATAGAGATCAACCCGTATCTTCTGGGTACCATGGCTGGGG
GTGCAGCGGATTGCAGCTTCTGGGAGCGGTTGTTGGCTCGGCAGTGTCGAATCTATGAGCTTCGCAAAAAGGAACGCATC
TCGGTCGCAGCAGCCTCTAAACTGCTCGCTAACATGGTGTATCAGTACAAAGGCATGGGGCTGTCCATGGGCACCATGAT
CTGTGGCTGGGATAAGAGAGGCCCTGGCCTCTACTACGTAGACAGCGAGGGGAACAGGATCTCTGGGACCGCCTTCTCAG
TGGGCTCTGGCTCCGTGTATGCTTACGGCGTTATGGATCGAGGCTACTCCTATGACCTGAAAGTGGAGGAGGCCTATGAT
CTGGCCCGCCGAGCCATCTAACAAGCCACCTACAGAGATGCCTACTCCGGAGGGGCAGTCAACCTCTACCACGTGCGGGA
GGATGGCTGGATCCGGGTGTCCAGTGACAATGTAGCTGACTTACATGACAAGTACAGTAGTGTATCTGTCCCC

Alignment

ORF - retro_mmus_2887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.49 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALASVLQRPMPVNQHGFFGLGGGADLLDLGPGSPGDGLSLAAPSWGVPEEPRIEMLHGTTTLAFKFLHG
          MALASVLQRPMPVNQHGFFGLGGGADLLDLGPGSP.DGLSLAAPSWGVPEEPRIEMLHGTTTLAFKFLHG
Retrocopy MALASVLQRPMPVNQHGFFGLGGGADLLDLGPGSPSDGLSLAAPSWGVPEEPRIEMLHGTTTLAFKFLHG

Parental  VIVAADSRATAGAYIASQ-TVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAAS
          VIVAADSRATAGAYIASQ.TVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELR.KERISVAAAS
Retrocopy VIVAADSRATAGAYIASQ>TVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRKKERISVAAAS

Parental  KLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGTAFSVGSGSVYAYGVMDRGYSYDLKVE
          KLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGTAFSVGSGSVYAYGVMDRGYSYDLKVE
Retrocopy KLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGTAFSVGSGSVYAYGVMDRGYSYDLKVE

Parental  EAYDLARRAIYQATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLHDKYSSVSVP
          EAYDLARRAI.QATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLHDKYSSVSVP
Retrocopy EAYDLARRAI*QATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLHDKYSSVSVP

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
SRP007412_brain	1.75 RPM	14.02 RPM
SRP007412_cerebellum	5.64 RPM	10.20 RPM
SRP007412_heart	0.25 RPM	25.62 RPM
SRP007412_kidney	7.35 RPM	16.25 RPM
SRP007412_liver	5.52 RPM	15.10 RPM
SRP007412_testis	7.32 RPM	14.32 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2887 was not detected

EST

14 EST(s) were mapped to retro_mmus_2887 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AV448513	3181086	3181524	99.1	432	4	426
AV482435	3181128	3181475	99.8	345	1	343
AV483294	3181107	3181466	99.2	351	1	345
AV511762	3181128	3181502	99.2	371	2	367
BY037384	3181069	3181448	99.3	375	3	371
BY039707	3181069	3181432	99.2	358	3	354
BY045698	3181069	3181458	98.8	383	5	377
BY047017	3181076	3181471	99.3	391	3	387
BY049826	3181070	3181479	99.3	405	3	401
BY051794	3181070	3181430	98.9	355	4	350
BY058803	3181070	3181458	99.5	385	2	382
BY303238	3181083	3181438	99.5	352	2	349
BY314825	3181087	3181458	99.5	368	2	365
BY339519	3181069	3181430	98.7	354	5	348

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_133977	271 libraries	150 libraries	97 libraries	167 libraries	387 libraries

The graphical summary, for retro_mmus_2887 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2887 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2887 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
Callithrix jacchus	ENSCJAG00000008299	4 retrocopies	retro_cjac_1983, retro_cjac_35, retro_cjac_3888, retro_cjac_4076,
Homo sapiens	ENSG00000100804	2 retrocopies	retro_hsap_1634, retro_hsap_95,
Gorilla gorilla	ENSGGOG00000026856	2 retrocopies	retro_ggor_1232, retro_ggor_156,
Latimeria chalumnae	ENSLACG00000015194	1 retrocopy	retro_lcha_3,
Macropus eugenii	ENSMEUG00000003572	1 retrocopy	retro_meug_28,
Myotis lucifugus	ENSMLUG00000014281	1 retrocopy	retro_mluc_1428,
Macaca mulatta	ENSMMUG00000006007	1 retrocopy	retro_mmul_1558,
Mus musculus	ENSMUSG00000022193	1 retrocopy	retro_mmus_2887 ,
Nomascus leucogenys	ENSNLEG00000014891	2 retrocopies	retro_nleu_1063, retro_nleu_2936,
Oryctolagus cuniculus	ENSOCUG00000013109	1 retrocopy	retro_ocun_176,
Pongo abelii	ENSPPYG00000005654	1 retrocopy	retro_pabe_171,
Sus scrofa	ENSSSCG00000002036	1 retrocopy	retro_sscr_616,