RetrogeneDB ID: retro_mmus_109

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:48046756..48048061(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000059040
• Aliases: Eno1b, EG433182, Eno1, Gm5506
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Eno1
• Ensembl ID: ENSMUSG00000063524
• Aliases: Eno1, 0610008I15, AL022784, Eno-1, MBP-1
• Description: enolase 1, alpha non-neuron [Source:MGI Symbol;Acc:MGI:95393]

Sequence

>retro_mmus_109
ATGTCTATTCTCAGGATCCACGCCAGAGAGATCTTTGACTCCCGTGGGAATCCCACTGTTGAGGTCGATCTGTACACCGC
AAAAGGTCTCTTCCGAGCTGCGGTGCCCAGCGGTGCGTCCACTGGCATCTACGAGGCCCTAGAACTCCGAGACAATGATA
AGACCCGCTTCATGGGGAAGGGTGTCTCACAGGCTGTTGAGCACATCAATAAAACTATTGCGCCTGCTCTGGTTAGCAAG
AAAGTGAATGTTGTGGAGCAAGAGAAGATTGACAAGCTGATGATCGAGATGGACGGCACAGAGAATAAATCTAAATTTGG
TGCAAATGCCATCCTGGGAGTGTCCCTGGCTGTCTGCAAAGCTGGTGCCGTGGAAAAGGGGGTGCCCCTTTACCGCCACA
TTGCTGACTTGGCCGGCAACCCTGAAGTCATCCTGCCTGTCCCGGCTTTCAATGTGATCAACGGTGGTTCTCATGCTGGC
AACAAGCTGGCCATGCAAGAGTTCATGATCCTGCCTGTGGGGGCATCCAGCTTCCGGGAAGCCATGCGCATTGGAGCAGA
GGTTTACCACAACCTGAAGAACGTGATCAAGGAGAAGTACGGGAAGGACGCCACCAATGTGGGTGATGAGGGTGGATTCG
CACCTAACATCCTGGAGAACAAAGAAGCACTGGAGCTGCTCAAGACTGCAATCGCAAAGGCCGGCTACACTGACCAGGTT
GTCATCGGCATGGATGTGGCTGCCTCTGAATTCTACAGGTCTGGCAAGTATGACCTGGACTTCAAGTCTCCGGATGACCC
CAGCAGGTACATCACGCCCGACCAGCTGGCTGATCTGTACAAGTCCTTCGTCCAGAACTACCCAGTGGTGTCCATCGAAG
ATCCCTTTGACCAGGACGACTGGGGCGCCTGGCAGAAGTTCACGGCTAGTGCGGGCATCCAGGTGGTGGGCGATGACCTC
ACAGTGACCAACCCTAAGCGGATTGCCAAGGCTGCGAGCGAGAAGTCCTGCAACTGCCTCTTGCTCAAAGTGAACCAGAT
CGGCTCCGTGACCGAGTCCCTGCAGGCGTGTAAGCTGGCCCAATCCAATGGCTGGGGCGTCATGGTGTCCCACCGATCTG
GGGAAACTGAGGACACTTTCATCGCAGACCTGGTGGTGGGGCTCTGCACTGGGCAGATCAAGACTGGTGCCCCTTGCCGA
TCCGAGCGCCTGGCCAAGTACAACCAGATCCTTAGAATTGAGGAAGAGCTGGGCAGCAAAGCCAAGTTTGCTGGCAGGTC
CTTCAGGAACCCCCTGGCCAAATAA

Alignment

ORF - retro_mmus_109 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  MSILRIHAREIFDSRGNPTVEVDLYTAKGLFRAAVPSGASTGIYEALELRDNDKTRFMGKGVSQAVEHIN
          MSILRIHAREIFDSRGNPTVEVDLYTAKGLFRAAVPSGASTGIYEALELRDNDKTRFMGKGVSQAVEHIN
Retrocopy MSILRIHAREIFDSRGNPTVEVDLYTAKGLFRAAVPSGASTGIYEALELRDNDKTRFMGKGVSQAVEHIN

Parental  KTIAPALVSKKVNVVEQEKIDKLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN
          KTIAPALVSKKVNVVEQEKIDKLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN
Retrocopy KTIAPALVSKKVNVVEQEKIDKLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN

Parental  PEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFREAMRIGAEVYHNLKNVIKEKYGKDATNVGDE
          PEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFREAMRIGAEVYHNLKNVIKEKYGKDATNVGDE
Retrocopy PEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFREAMRIGAEVYHNLKNVIKEKYGKDATNVGDE

Parental  GGFAPNILENKEALELLKTAIAKAGYTDQVVIGMDVAASEFYRSGKYDLDFKSPDDPSRYITPDQLADLY
          GGFAPNILENKEALELLKTAIAKAGYTDQVVIGMDVAASEFYRSGKYDLDFKSPDDPSRYITPDQLADLY
Retrocopy GGFAPNILENKEALELLKTAIAKAGYTDQVVIGMDVAASEFYRSGKYDLDFKSPDDPSRYITPDQLADLY

Parental  KSFVQNYPVVSIEDPFDQDDWGAWQKFTASAGIQVVGDDLTVTNPKRIAKAASEKSCNCLLLKVNQIGSV
          KSFVQNYPVVSIEDPFDQDDWGAWQKFTASAGIQVVGDDLTVTNPKRIAKAASEKSCNCLLLKVNQIGSV
Retrocopy KSFVQNYPVVSIEDPFDQDDWGAWQKFTASAGIQVVGDDLTVTNPKRIAKAASEKSCNCLLLKVNQIGSV

Parental  TESLQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQILRIEEELGSK
          TESLQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQILRIEEELGSK
Retrocopy TESLQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQILRIEEELGSK

Parental  AKFAGRSFRNPLAK
          AKFAGRSFRNPLAK
Retrocopy AKFAGRSFRNPLAK

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	2.57 RPM	168.31 RPM
SRP007412_cerebellum	12.07 RPM	89.36 RPM
SRP007412_heart	0.00 RPM	56.41 RPM
SRP007412_kidney	12.92 RPM	150.47 RPM
SRP007412_liver	12.48 RPM	106.07 RPM
SRP007412_testis	11.89 RPM	73.55 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_109 was not detected

EST

No EST(s) were mapped for retro_mmus_109 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_59637	66 libraries	91 libraries	589 libraries	264 libraries	62 libraries

The graphical summary, for retro_mmus_109 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_109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_109 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003483	2 retrocopies	retro_chof_1289, retro_chof_1811,
Callithrix jacchus	ENSCJAG00000000359	4 retrocopies	retro_cjac_1963, retro_cjac_2238, retro_cjac_3891, retro_cjac_438,
Erinaceus europaeus	ENSEEUG00000008602	2 retrocopies	retro_eeur_23, retro_eeur_243,
Homo sapiens	ENSG00000074800	1 retrocopy	retro_hsap_325,
Macropus eugenii	ENSMEUG00000005942	11 retrocopies	retro_meug_1445, retro_meug_1521, retro_meug_353, retro_meug_472, retro_meug_494, retro_meug_652, retro_meug_664, retro_meug_765, retro_meug_794, retro_meug_874, retro_meug_888,
Macropus eugenii	ENSMEUG00000007840	1 retrocopy	retro_meug_96,
Monodelphis domestica	ENSMODG00000009521	1 retrocopy	retro_mdom_1794,
Mustela putorius furo	ENSMPUG00000006382	2 retrocopies	retro_mputfur_1162, retro_mputfur_547,
Mus musculus	ENSMUSG00000063524	1 retrocopy	retro_mmus_109 ,
Oryctolagus cuniculus	ENSOCUG00000010086	1 retrocopy	retro_ocun_933,
Otolemur garnettii	ENSOGAG00000004001	1 retrocopy	retro_ogar_1059,
Ochotona princeps	ENSOPRG00000009492	1 retrocopy	retro_opri_969,
Pan troglodytes	ENSPTRG00000000109	1 retrocopy	retro_ptro_261,
Pteropus vampyrus	ENSPVAG00000005030	1 retrocopy	retro_pvam_317,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304,
Tarsius syrichta	ENSTSYG00000002509	1 retrocopy	retro_tsyr_2011,