RetrogeneDB ID: retro_rnor_112

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:65883767..65885072(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000028543
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Eno1
• Ensembl ID: ENSRNOG00000017895
• Aliases: Eno1, Nne
• Description: Alpha-enolase [Source:UniProtKB/Swiss-Prot;Acc:P04764]

Sequence

>retro_rnor_112
ATGTCCATTCTCAAGATCCATGCCAGAGAGATCTTTGACTCCCGCGGGAATCCCACCGTTGAGGTGGATCTCTACACCGC
AAAAGGTCTCTTCCGTGCTGCGGTGCCCAGCGGTGCGTCCACTGGCATCTACGAGGCCCTAGAACTCCGAGACAATGATA
AGACCCGCTTCATGGGGAAGGGTGTCTCAAAGGCTGTTGAGCACATCAATAAAACTATTGCACCTGCTCTGGTTAGCAAG
AAACTGAATGTTGTGGAGCAGGAGAAGATTGACCAGCTGATGATCGAGATGGACGGCACAGAGAATAAATCTAAGTTTGG
TGCAAATGCCATCCTGGGAGTGTCCCTGGCTGTCTGCAAGGCTGGTGCCGTGGAGAAGGGGGTGCCCCTTTACCGTCACA
TTGCCGACTTGGCCGGCAACCCTGAAGTCATCCTGCCGGTCCCAGCTTTCAATGTGATCAACGGCGGTTCTCATGCTGGC
AACAAGCTGGCCATGCAAGAGTTCATGATCCTGCCTGTGGGGGCATCCTCTTTCCGGGAAGCCATGCGCATTGGAGCAGA
GGTTTACCACAACCTGAAGAACGTCATCAAGGAGAAGTACGGGAAAGACGCCACCAATGTGGGTGATGAGGGTGGATTCG
CACCTAACATCCTGGAGAACAAAGAAGCACTGGAGCTGCTCAAGTCTGCCATTGCAAAGGCCGGCTACACTGACCAGGTT
GTCATCGGCATGGATGTGGCTGCCTCCGAGTTCTACAGGGCTGGCAAGTATGACCTGGACTTCAAGTCTCCAGATGATGC
CAGCCGATACATCACACCCGACCAGCTGGCCGACCTGTACAAGTCCTTCATCAAGGACTACCCAGTGGTGTCCATTGAAG
ATCCCTTTGACCAGGACGACTGGGATGCTTGGCAGAAGTTCACAGCTACTGCAGGCATCCAGGTGGTGGGGGATGACCTC
ACAGTGACCAACCCTAAGCGGATCGCCAAGGCTGCAGGCGAGAAGTCCTGCAACTGCCTCCTGCTCAAAGTGAACCAGAT
TGGCTCTGTGACCGAGTCTCTGCAGGCGTGTAAGCTCGCCCAGTCCAATGGCTGGGGTGTCATGGTGTCCCATCGATCTG
GGGAGACTGAGGACACTTTCATTGCCGACCTGGTGGTGGGGCTCTGCACTGGGCAGATCAAGACTGGTGCCCCCTGCCGA
TCTGAGTGCCTGGCCAAGTACAATCAGATCCTTAGAATCGAGGAGGAGCTGGGCAGCAAAGCCAAGTTTGCCGGCAGGTC
CTTCAGGAACCCCCTGGCCAAGTAA

Alignment

ORF - retro_rnor_112 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSILKIHAREIFDSRGNPTVEVDLYTAKGLFRAAVPSGASTGIYEALELRDNDKTRFMGKGVSKAVEHIN
          MSILKIHAREIFDSRGNPTVEVDLYTAKGLFRAAVPSGASTGIYEALELRDNDKTRFMGKGVSKAVEHIN
Retrocopy MSILKIHAREIFDSRGNPTVEVDLYTAKGLFRAAVPSGASTGIYEALELRDNDKTRFMGKGVSKAVEHIN

Parental  KTIAPALVSKKLNVVEQEKIDQLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN
          KTIAPALVSKKLNVVEQEKIDQLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN
Retrocopy KTIAPALVSKKLNVVEQEKIDQLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN

Parental  PEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFREAMRIGAEVYHNLKNVIKEKYGKDATNVGDE
          PEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFREAMRIGAEVYHNLKNVIKEKYGKDATNVGDE
Retrocopy PEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFREAMRIGAEVYHNLKNVIKEKYGKDATNVGDE

Parental  GGFAPNILENKEALELLKSAIAKAGYTDQVVIGMDVAASEFYRAGKYDLDFKSPDDASRYITPDQLADLY
          GGFAPNILENKEALELLKSAIAKAGYTDQVVIGMDVAASEFYRAGKYDLDFKSPDDASRYITPDQLADLY
Retrocopy GGFAPNILENKEALELLKSAIAKAGYTDQVVIGMDVAASEFYRAGKYDLDFKSPDDASRYITPDQLADLY

Parental  KSFIKDYPVVSIEDPFDQDDWDAWQKFTATAGIQVVGDDLTVTNPKRIAKAAGEKSCNCLLLKVNQIGSV
          KSFIKDYPVVSIEDPFDQDDWDAWQKFTATAGIQVVGDDLTVTNPKRIAKAAGEKSCNCLLLKVNQIGSV
Retrocopy KSFIKDYPVVSIEDPFDQDDWDAWQKFTATAGIQVVGDDLTVTNPKRIAKAAGEKSCNCLLLKVNQIGSV

Parental  TESLQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQILRIEEELGSK
          TESLQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSE.LAKYNQILRIEEELGSK
Retrocopy TESLQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSECLAKYNQILRIEEELGSK

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
SRP017611_brain	0.29 RPM	329.43 RPM
SRP017611_kidney	0.84 RPM	662.23 RPM
SRP017611_liver	0.00 RPM	127.01 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_rnor_112 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
FM062233	65883734	65884305	99.5	567	2	563

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_112 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 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	ENSRNOG00000004078	1 retrocopy	retro_rnor_2228,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112 ,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304,
Tarsius syrichta	ENSTSYG00000002509	1 retrocopy	retro_tsyr_2011,