RetrogeneDB ID: retro_mmus_135

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:62071122..62072361(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000046687
• Aliases: Gm5424, EG432466
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ass1
• Ensembl ID: ENSMUSG00000076441
• Aliases: Ass1, AA408052, ASS, Ass-1, fold
• Description: argininosuccinate synthetase 1 [Source:MGI Symbol;Acc:MGI:88090]

Sequence

>retro_mmus_135
ATGTCCAGCAAGGGCTCTGTGGTTCTGGCCTACAGTGGTGGCCTGGACACCTCCTGCATCCTCGTGTGGCTGAAGGAACA
AGGCTATGATGTCATCGCCTACCTGGCCAACATTGGCCAGAAGGAAGACTTTGAGGAAGCCAGGAAGAAGGCGCTGAAGC
TTGGGGCCAAAAAGGTGTTCATTGAGGATGTGAGCAAGGAATTTGTGGAAGAGTTCATCTGGCCTGCTGTCCAGTCCAGT
GCACTCTACGAGGACCGCTATCTCCTGGGCACCTCTCTCGCCAGGCCTTGCATAGCTCGCAGACAGGTGGAGATTGCCCA
GCGTGAAGGGGCCAAGTATGTGTCTCACGGCGCCACGGGAAAGGGGAATGACCAGGTCCGCTTTGAGCTCACCTGCTACT
CACTGGCACCCCAGATTAAGGTCATCGCCCCCTGGAGGATGCCTGAGTTTTACAACCGGTTCAAGGGCCGAAATGATCTG
ATGGAGTATGCAAAGCAACACGGAATCCCCATCCCTGTCTCCCCCAAGAGCCCCTGGAGTATGGATGAAAACCTCATGCA
CATCAGCTATGAGGCTGGGATCCTGGAAAACCCCAAGAATCAAGCACCTCCGGGTCTCTACACAAAAACTCAGGACCCTG
CCAAAGCACCCAACACCCCAGATGTCCTTGAGATAGAATTCAAAAAAGGGGTCCCTGTGAAGGTGACCAACATCAAAGAT
GGCACAACCCGCACCACATCCCTGGAACTCTTCATGTACCTGAACGAAGTTGCGGGCAAGCACGGAGTGGGTCGCATTGA
CATCGTGGAGAACCGCTTCATTGGAATGAAGTCCCGAGGTATCTACGAGACCCCAGCAGGGACCATCCTTTACCACGCTC
ATTTAGACATAGAGGCCTTCACGATGGATCGGGAAGTACGCAAAATCAAGCAGGGCCTGGGCCTCAAATTCGCAGAGCTC
GTATACACAGGTTTCTGGCACAGCCCTGAATGTGAATTTGTTCGCCACTGCATCCAGAAGTCCCAGGAGCGGGTAGAAGG
GAAGGTGCAGGTGTCTGTCTTCAAGGGCCAAGTGTACATCCTCGGTCGGGAGTCTCCACTTTCACTCTACAATGAAGAGC
TGGTGAGCATGAACGTGCAGGGTGACTATGAGCCCATCGACGCCACTGGCTTCATCAATATCAACTCGCTCAGGCTGAAG
GAGTACCATCGCCTTCAGAGCAAGGTCACTGCCAAATAG

Alignment

ORF - retro_mmus_135 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSKGSVVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFEEARKKALKLGAKKVFIEDVSKEFVE
          MSSKGSVVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFEEARKKALKLGAKKVFIEDVSKEFVE
Retrocopy MSSKGSVVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFEEARKKALKLGAKKVFIEDVSKEFVE

Parental  EFIWPAVQSSALYEDRYLLGTSLARPCIARRQVEIAQREGAKYVSHGATGKGNDQVRFELTCYSLAPQIK
          EFIWPAVQSSALYEDRYLLGTSLARPCIARRQVEIAQREGAKYVSHGATGKGNDQVRFELTCYSLAPQIK
Retrocopy EFIWPAVQSSALYEDRYLLGTSLARPCIARRQVEIAQREGAKYVSHGATGKGNDQVRFELTCYSLAPQIK

Parental  VIAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPVTPKSPWSMDENLMHISYEAGILENPKNQAPPGLYTKT
          VIAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPV.PKSPWSMDENLMHISYEAGILENPKNQAPPGLYTKT
Retrocopy VIAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPVSPKSPWSMDENLMHISYEAGILENPKNQAPPGLYTKT

Parental  QDPAKAPNSPDVLEIEFKKGVPVKVTNIKDGTTRTTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSRG
          QDPAKAPN.PDVLEIEFKKGVPVKVTNIKDGTTRTTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSRG
Retrocopy QDPAKAPNTPDVLEIEFKKGVPVKVTNIKDGTTRTTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSRG

Parental  IYETPAGTILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIQKSQERVEGKVQ
          IYETPAGTILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIQKSQERVEGKVQ
Retrocopy IYETPAGTILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIQKSQERVEGKVQ

Parental  VSVFKGQVYILGRESPLSLYNEELVSMNVQGDYEPIDATGFININSLRLKEYHRLQSKVTAK
          VSVFKGQVYILGRESPLSLYNEELVSMNVQGDYEPIDATGFININSLRLKEYHRLQSKVTAK
Retrocopy VSVFKGQVYILGRESPLSLYNEELVSMNVQGDYEPIDATGFININSLRLKEYHRLQSKVTAK

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	0.14 RPM	13.29 RPM
SRP007412_cerebellum	0.09 RPM	7.34 RPM
SRP007412_heart	0.00 RPM	2.12 RPM
SRP007412_kidney	15.05 RPM	584.63 RPM
SRP007412_liver	21.52 RPM	1275.99 RPM
SRP007412_testis	0.05 RPM	13.95 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_135 was not detected

EST

No EST(s) were mapped for retro_mmus_135 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_4382	147 libraries	108 libraries	307 libraries	148 libraries	362 libraries
TSS #2	TSS_4383	851 libraries	172 libraries	31 libraries	13 libraries	5 libraries
TSS #3	TSS_4384	799 libraries	210 libraries	43 libraries	15 libraries	5 libraries

The graphical summary, for retro_mmus_135 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_135 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_135 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020554	3 retrocopies	retro_cjac_1219, retro_cjac_4038, retro_cjac_4209,
Homo sapiens	ENSG00000130707	14 retrocopies	retro_hsap_2247, retro_hsap_2885, retro_hsap_3109, retro_hsap_3175, retro_hsap_3252, retro_hsap_3564, retro_hsap_3824, retro_hsap_4149, retro_hsap_4182, retro_hsap_4648, retro_hsap_4743, retro_hsap_4934, retro_hsap_820, retro_hsap_985,
Gorilla gorilla	ENSGGOG00000010228	8 retrocopies	retro_ggor_1346, retro_ggor_1675, retro_ggor_2134, retro_ggor_2403, retro_ggor_2574, retro_ggor_2787, retro_ggor_671, retro_ggor_787,
Myotis lucifugus	ENSMLUG00000006066	2 retrocopies	retro_mluc_1058, retro_mluc_1304,
Mus musculus	ENSMUSG00000076441	1 retrocopy	retro_mmus_135 ,
Nomascus leucogenys	ENSNLEG00000012500	13 retrocopies	retro_nleu_1088, retro_nleu_1245, retro_nleu_1317, retro_nleu_1381, retro_nleu_1390, retro_nleu_1424, retro_nleu_1701, retro_nleu_1792, retro_nleu_220, retro_nleu_253, retro_nleu_2680, retro_nleu_2764, retro_nleu_625,
Pongo abelii	ENSPPYG00000019692	13 retrocopies	retro_pabe_1963, retro_pabe_2390, retro_pabe_2637, retro_pabe_2696, retro_pabe_2937, retro_pabe_3069, retro_pabe_3197, retro_pabe_3422, retro_pabe_3460, retro_pabe_3521, retro_pabe_3522, retro_pabe_731, retro_pabe_834,
Pan troglodytes	ENSPTRG00000021473	14 retrocopies	retro_ptro_1590, retro_ptro_1951, retro_ptro_2101, retro_ptro_2199, retro_ptro_2268, retro_ptro_2421, retro_ptro_2602, retro_ptro_2821, retro_ptro_2836, retro_ptro_3064, retro_ptro_3158, retro_ptro_3298, retro_ptro_571, retro_ptro_762,