RetrogeneDB ID: retro_mmus_21

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:113314675..113315422(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000058126
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Tpm3
• Ensembl ID: ENSMUSG00000027940
• Aliases: Tpm3, Tm5NM, Tpm-5, Tpm5, Trop-5, gamma-TM, hTM30nm, hTMnm
• Description: tropomyosin 3, gamma [Source:MGI Symbol;Acc:MGI:1890149]

Sequence

>retro_mmus_21
ATGGCCGGGACCACCACCATCGAGGCGGTAAAGCGCAAGATCCAGGTTCTGCAGCAGCAAGCTGATGATGCAGAGGAAAG
GGCCGAGCGCCTCCAGCAGGAAGTGGAGGGAGAAAGGCGGGCCCGGAAGCAGGCTGAAGCTGAGGTGGCCTCCTTGAACC
GCAGGATCCAGCTGGTTGAAGAGGAGCTGGACCGTGCGCAGGAGCGCCTTGCCACTGCTTTGCAGAAGCTGGAGGAAGCA
GAGAAGGCTGCTGATGAGAGTGAGAGAGGTATGAAGGTGATTGAAAATCGGGCTCTAAAAGATGAAGAAAAGATGGAACT
CCAGGAAATCCAGCTAAAGGAAGCAAAGCACATTGCAGAAGAGGCCGATAGGAAGTATGAAGAGGTGGCTCGTAAGTTGG
TGATTATTGAAGGAGACTTGGAACGCACGGAGGAACGTGCTGAGCTGGCAGAGTCCCGTTGCCGAGAGATGGATGAACAG
ATCAGACTGATGGACCAGAACCTGAAGTGTCTGAGTGCTGCTGAAGAAAAGTACTCTCAAAAAGAAGACAAGTATGAAGA
AGAAATAAAGATTCTTACTGATAAACTCAAGGAGGCAGAGACCCGTGCTGAGTTTGCTGAAAGATCGGTAGCCAAGCTGG
AGAAGACCATTGATGACCTGGAAGATAAACTGAAGTGCACCAAAGAGGAGCATCTCTGTACACAAAGGATGCTGGACCAG
ACCCTGCTGGACCTGAACGAGATGTAG

Alignment

ORF - retro_mmus_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGTTTIEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL
          MAGTTTIEAVKRKIQVLQQQADDAEERAERLQ.EVEGERRAR.QAEAEVASLNRRIQLVEEELDRAQERL
Retrocopy MAGTTTIEAVKRKIQVLQQQADDAEERAERLQQEVEGERRARKQAEAEVASLNRRIQLVEEELDRAQERL

Parental  ATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDL
          ATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDL
Retrocopy ATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDL

Parental  ERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSV
          ERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSV
Retrocopy ERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSV

Parental  AKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
          AKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
Retrocopy AKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM

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	1.07 RPM	69.20 RPM
SRP007412_cerebellum	3.04 RPM	48.59 RPM
SRP007412_heart	0.22 RPM	34.40 RPM
SRP007412_kidney	4.56 RPM	59.56 RPM
SRP007412_liver	1.99 RPM	38.18 RPM
SRP007412_testis	3.89 RPM	37.05 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_21 was not detected

EST

No EST(s) were mapped for retro_mmus_21 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_32430	271 libraries	534 libraries	260 libraries	4 libraries	3 libraries

The graphical summary, for retro_mmus_21 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_21 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_21 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011877	2 retrocopies	retro_amel_1017, retro_amel_1212,
Bos taurus	ENSBTAG00000033217	3 retrocopies	retro_btau_1166, retro_btau_210, retro_btau_933,
Canis familiaris	ENSCAFG00000017311	4 retrocopies	retro_cfam_1278, retro_cfam_1678, retro_cfam_2089, retro_cfam_983,
Cavia porcellus	ENSCPOG00000007279	1 retrocopy	retro_cpor_150,
Dasypus novemcinctus	ENSDNOG00000019156	7 retrocopies	retro_dnov_1322, retro_dnov_1767, retro_dnov_329, retro_dnov_451, retro_dnov_848, retro_dnov_878, retro_dnov_944,
Equus caballus	ENSECAG00000010942	1 retrocopy	retro_ecab_390,
Felis catus	ENSFCAG00000012596	1 retrocopy	retro_fcat_1441,
Homo sapiens	ENSG00000143549	9 retrocopies	retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011, retro_hsap_2012, retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Myotis lucifugus	ENSMLUG00000013331	1 retrocopy	retro_mluc_1038,
Macaca mulatta	ENSMMUG00000010805	10 retrocopies	retro_mmul_1019, retro_mmul_1240, retro_mmul_1384, retro_mmul_1385, retro_mmul_1703, retro_mmul_1829, retro_mmul_2128, retro_mmul_2354, retro_mmul_314, retro_mmul_880,
Mustela putorius furo	ENSMPUG00000007875	1 retrocopy	retro_mputfur_604,
Mus musculus	ENSMUSG00000027940	1 retrocopy	retro_mmus_21 ,
Mus musculus	ENSMUSG00000031799	1 retrocopy	retro_mmus_1625,
Oryctolagus cuniculus	ENSOCUG00000011821	2 retrocopies	retro_ocun_699, retro_ocun_8,