RetrogeneDB ID: retro_ptro_261

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:215791527..215792828(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ENO1
• Ensembl ID: ENSPTRG00000000109
• Aliases: None
• Description: Pan troglodytes enolase 1, (alpha) (ENO1), mRNA. [Source:RefSeq mRNA;Acc:NM_001220779]

Sequence

>retro_ptro_261
ATGTCTATTCTCAAGATCCATGCCAGGGAGATCTTTGACTCTCGTGGGAATCCCACTGTTGAGGTTGATCTCTTCACCTC
AGAAGGTCTCTTCAGAGCTGCTGTGCCCAGTGGTGCTTCAACTGGTATCTATGAGGTCCTAGAGCTCCAGGACAATGATA
AGACTCACTATATGGGGAAGGGTGTCTCAAAGCCTGTTGAGCCCATCAATAAAACTATTGCACCTGTCCTGGTTAGCAAG
AAACTGAACGTCACAGAACAAGAGAAGATTGACAAACTTATGATAGAGATGGATGAAACAGAAAATAAATCTAAATTTGG
TGCAAACGCCATTCTGGGAGTGTCCCTCGCTGCCTGCAAAGCTAGTGCTGTTGAGAAGGGGGTTCCCCTGTACCACCACA
TCGCCGACTTGTCTGGCAACTCCAAAGTCATCTTGCCAGTCCCGGTGTTCAGTGTCATCAATGGCAGTTCTCATGCTGTC
ACCAAGCTGGCCATGCAGGAGTTCATGGTCCTCCCAGTCGGTGCAGCAAACTTCAGGGAAGCCATGCCCATTGGAGCGGA
GGTTTACCACAGCCTGAAGAATGTCATCAAGGAGAAATATGGGAAAGATGCCACCGGTGTGGGGGATGGAGGCGCGTTTG
CTCCCAGCATCCTGGAGAATAAAGAAGGCCTGGAGCTGCTGAAGACTGCGATTGGGAAAGCTGGCTACACTGATAAGGTG
ATCGTCGGCATGGACGTAGCGGCCTCCGAGTTCTTCAGGTCTGGAAAGTATGACCTGGAATTCAAGTTTCTCCACGACCC
CACCAGGTACATCTCACCTGACTGTCTGGCTGACCTGTACAAGTCCTTCATCAAAAACTACCCAGTGGTGTCTACTGAAG
ATCCCTTTGACCAGGATGACTGGGGAGCTTGGCAGAAGTTCACGGCCAGTGCAGGAATCCAGGTAGTGGGGGATGATCTC
AGAGTGACCAACCCAAAGAGGACAGCCTCGGCCGTGAATGAGAAGAAGTGCACTGCCTTCTGCTCAAAGTGAACCAGATT
CGCTCCGTGACTGAGTCCCTTCAGGCATGCAAGCTGGCCCAGGCCAATGGTTGGTGTGTCATGGTGCCTCATCATTCTGG
GGAGACTGAAAATACCTTCATCACTGACCTGGTGGTGGGGCTGTGACCTGGGCAGCTCAAGACTGGTGCCCCTTGCTGAT
CTCAGCGCTTGGCCAAGTACAACCAGCTCCTCAGAATTGAAGAGGAGCTGGGCAGCAAGGCTAAGTTTGCCGGCAGGAAC
TTCAGAAACCCCCCAGCCAAG

Alignment

ORF - retro_ptro_261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSILKIHAREIFDSRGNPTVEVDLFTSKGLFRAAVPSGASTGIYEALELRDNDKTRYMGKGVSKAVEHIN
          MSILKIHAREIFDSRGNPTVEVDLFTS.GLFRAAVPSGASTGIYE.LEL.DNDKT.YMGKGVSK.VE.IN
Retrocopy MSILKIHAREIFDSRGNPTVEVDLFTSEGLFRAAVPSGASTGIYEVLELQDNDKTHYMGKGVSKPVEPIN

Parental  KTIAPALVSKKLNVTEQEKIDKLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN
          KTIAP.LVSKKLNVTEQEKIDKLMIEMD.TENKSKFGANAILGVSLA.CKA.AVEKGVPLY.HIADL.GN
Retrocopy KTIAPVLVSKKLNVTEQEKIDKLMIEMDETENKSKFGANAILGVSLAACKASAVEKGVPLYHHIADLSGN

Parental  SEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGAANFREAMRIGAEVYHNLKNVIKEKYGKDATNVGDE
          S.VILPVP.F.VING.SHA..KLAMQEFM.LPVGAANFREAM.IGAEVYH.LKNVIKEKYGKDAT.VGD.
Retrocopy SKVILPVPVFSVINGSSHAVTKLAMQEFMVLPVGAANFREAMPIGAEVYHSLKNVIKEKYGKDATGVGDG

Parental  GGFAPNILENKEGLELLKTAIGKAGYTDKVVIGMDVAASEFFRSGKYDLDFKSPDDPSRYISPDQLADLY
          G.FAP.ILENKEGLELLKTAIGKAGYTDKV..GMDVAASEFFRSGKYDL.FK...DP.RYISPD.LADLY
Retrocopy GAFAPSILENKEGLELLKTAIGKAGYTDKVIVGMDVAASEFFRSGKYDLEFKFLHDPTRYISPDCLADLY

Parental  KSFIKDYPVVSIEDPFDQDDWGAWQKFTASAGIQVVGDDLTVTNPKRIAKAVNEKSC-NCLLLKVNQIGS
          KSFIK.YPVVS.EDPFDQDDWGAWQKFTASAGIQVVGDDL.VTNPKR.A.AVNEK.C..CLLLKVNQI.S
Retrocopy KSFIKNYPVVSTEDPFDQDDWGAWQKFTASAGIQVVGDDLRVTNPKRTASAVNEKKC<HCLLLKVNQIRS

Parental  VTESLQACKLAQANGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLLRIEEELGS
          VTESLQACKLAQANGW.VMV.H.SGETE.TFI.DLVVGL..GQ.KTGAPC.S.RLAKYNQLLRIEEELGS
Retrocopy VTESLQACKLAQANGWCVMVPHHSGETENTFITDLVVGL*PGQLKTGAPC*SQRLAKYNQLLRIEEELGS

Parental  KAKFAGRNFRNPLAK
          KAKFAGRNFRNP.AK
Retrocopy KAKFAGRNFRNPPAK

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_prefrontal_cortex	1.11 RPM	472.49 RPM
SRP007412_cerebellum	2.15 RPM	415.52 RPM
SRP007412_heart	1.43 RPM	91.99 RPM
SRP007412_kidney	9.26 RPM	866.83 RPM
SRP007412_liver	4.26 RPM	1096.73 RPM
SRP007412_testis	5.16 RPM	210.77 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_261 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_261 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_261 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_325

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 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,
Mus musculus	ENSMUSG00000063524	1 retrocopy	retro_mmus_109,
Otolemur garnettii	ENSOGAG00000004001	1 retrocopy	retro_ogar_1059,
Ochotona princeps	ENSOPRG00000009492	1 retrocopy	retro_opri_969,
Pan troglodytes	ENSPTRG00000000109	1 retrocopy	retro_ptro_261 ,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304,