RetrogeneDB ID: retro_mmus_188

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:120762888..120763212(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000078249
• Aliases: Hmga1-rs1, ENSMUSG00000041059, Hmgi-rs1
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Hmga1
• Ensembl ID: ENSMUSG00000046711
• Aliases: Hmga1, AL023995, Hmga1a, Hmga1b, Hmgi, Hmgiy, Hmgy
• Description: high mobility group AT-hook 1 [Source:MGI Symbol;Acc:MGI:96160]

Sequence

>retro_mmus_188
ATGAGCGAGTCGGGCTCAAAGTCCAGCCAGCCCCTGGCCTCCAAGCAGGAAAAGGATGGGACTGAGAAGCGAGGCCGGGG
CAGGCCACGCAAGCAGCCTCCGGTGAGTCCTGGGACGGCGCTGGTCGGGAGTCAGAAAGAGCCCAGTGAAGTGCCAACTC
CGAAGAGACCTCGGGGCCGACCAAAGGGAAGCAAGAATAAGGGCGCCGCCAAGACCCGGAAAGTCACCACAGCTCCAGGG
AGGAAACCAAGGGGCAGACCCAAGAAACTGGAGAAGGAGGAAGAGGAGGGCATCTCCCAGGAGTCCTCTGAGGAGGAGCA
GTGA

Alignment

ORF - retro_mmus_188 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MSESGSKSSQPLASKQEKDGTEKRGRGRPRKQPPVSPGTALVGSQKEPSEVPTPKRPRGRPKGSKNKGAA
          MSESGSKSSQPLASKQEKDGTEKRGRGRPRKQPPVSPGTALVGSQKEPSEVPTPKRPRGRPKGSKNKGAA
Retrocopy MSESGSKSSQPLASKQEKDGTEKRGRGRPRKQPPVSPGTALVGSQKEPSEVPTPKRPRGRPKGSKNKGAA

Parental  KTRKVTTAPGRKPRGRPKKLEKEEEEGISQESSEEEQ
          KTRKVTTAPGRKPRGRPKKLEKEEEEGISQESSEEEQ
Retrocopy KTRKVTTAPGRKPRGRPKKLEKEEEEGISQESSEEEQ

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	0.05 RPM	7.80 RPM
SRP007412_cerebellum	0.09 RPM	7.43 RPM
SRP007412_heart	0.09 RPM	11.30 RPM
SRP007412_kidney	0.10 RPM	2.89 RPM
SRP007412_liver	0.05 RPM	2.84 RPM
SRP007412_testis	0.05 RPM	6.63 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_188 was not detected

EST

No EST(s) were mapped for retro_mmus_188 retrocopy.

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_11022	532 libraries	361 libraries	174 libraries	4 libraries	1 library
TSS #2	TSS_11023	429 libraries	370 libraries	224 libraries	28 libraries	21 libraries

The graphical summary, for retro_mmus_188 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_188 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_188 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001061	1 retrocopy	retro_amel_1637,
Callithrix jacchus	ENSCJAG00000015226	2 retrocopies	retro_cjac_1197, retro_cjac_3158,
Homo sapiens	ENSG00000137309	4 retrocopies	retro_hsap_1175, retro_hsap_2277, retro_hsap_4663, retro_hsap_695,
Myotis lucifugus	ENSMLUG00000010085	2 retrocopies	retro_mluc_1619, retro_mluc_2429,
Macaca mulatta	ENSMMUG00000019529	2 retrocopies	retro_mmul_1276, retro_mmul_2406,
Mus musculus	ENSMUSG00000046711	1 retrocopy	retro_mmus_188 ,
Nomascus leucogenys	ENSNLEG00000008303	1 retrocopy	retro_nleu_1097,
Procavia capensis	ENSPCAG00000016076	1 retrocopy	retro_pcap_236,
Pongo abelii	ENSPPYG00000029838	4 retrocopies	retro_pabe_1941, retro_pabe_2441, retro_pabe_3623, retro_pabe_960,
Pan troglodytes	ENSPTRG00000040884	6 retrocopies	retro_ptro_1611, retro_ptro_2053, retro_ptro_3098, retro_ptro_499, retro_ptro_789, retro_ptro_807,
Pteropus vampyrus	ENSPVAG00000014283	1 retrocopy	retro_pvam_116,
Rattus norvegicus	ENSRNOG00000000488	1 retrocopy	retro_rnor_164,