RetrogeneDB ID: retro_nleu_1526

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397297.1:22005373..22006617(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000015824
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OLA1
• Ensembl ID: ENSNLEG00000005817
• Aliases: None
• Description: None

Sequence

>retro_nleu_1526
GCAGGACCTTTCTCTCGCTGCTACTGGGACCCTGTGTCATAGCCCAGGCTGAGCACGATGCCCCCTAAAAAGGGAGGTGA
TGGAATTAAACCACCCCCAATCATTGGAAGATTTGGAACCTCACTGAAAATTGGTATTGTTGGATTGCCAAATGTTGGGA
AATTTACTTTCTTCAATATATTAACCAATAGTCAGGCTTCAGCAGAAAACTTCCCATTCTGCACTATTGATCCTAATGAG
AGCAGAGTACCTGTGCCAGATGAAAGGTTTGACTTTCTTTGCCAATATCACAAACCAGCAAGCAAAATTCCTGCCTTTCT
AAATGTAGTGGATATTGCTGGCCTTGTGAAAGGAGCTCACAATGGGCAGGGCCTGGGGAATGCTTTTTTATCTCATTTTA
GTGCTTGTGATGGCATTTTCATCTAACACGTGCTTTTGAAGATGATGATATCACGCATGTTGAAGAAAGTGTAGATCCTA
TTCGAGATATAGAAATAATACATGAAGAGCTTCAGCTTAAAGATGAGGAAATGATTGGGCCCATTATAGATAAACTAGAA
AAGGTGGCTGTGAGAGGAGGAGATAAAAAACTAAAACCTGAATATGATATAACGTGCAAAGTAAAATCCTGGGTTATAGA
TCAAAAGAAACCTGTTCCCTTCTATCATGATTGGAATGACAAAGAGATTGAAGTGTTGAATAAACATTTATTTTTGACTT
CAAAACCAATGGTCTACTTGGTTAATCTTTCTGAAAAAGACTACATTAGAAAGAAAAACAAATGGTTGATAAAAATTAAA
GAGTGGGTGGACAAGTATGACCCAGGTGCCTTGGTCATTCCTTTTAGTGGGGCCTTGGAACTCAAGTTGCAAGAATTGAG
TGCTGAGGAGAGACAGCAGTATCTGGAAGCGAACATGACACAAAGTGCTTTGCCAAAGATCATTAAGGCTGGGTTTGCAG
CACTCCAACTAGAATACTTTTTCACTGCAGGCCCAGATGAAGTGCGTGCATGGACCATCAGGAAAGGGACAAAGGCTCCT
CAGGCTGCAGGAAAGATTCACACAGATTTTGAAAAGGGATTCATTATGGCTGAAGTAGTGAAATACGACGATTTTAAAGA
GGAAGGTTCTGAAAATGCAGTCAAGGCTGCTGGAAAGTACAGACAACAAGGCAGAAATTATATTGTTGAAGATGGAGATA
CTATCTTCTTCAAATTTAACACACCTCAACAACTGAAGAAGAAA

Alignment

ORF - retro_nleu_1526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.67 %
• Parental protein coverage: 90.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGPFFRCRCDPVSSPRPSTMPPKKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAEN
          AGPF.RC..DPVS.PR.STMPPKKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGK.TFFN.LTNSQASAEN
Retrocopy AGPFSRCYWDPVS*PRLSTMPPKKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKFTFFNILTNSQASAEN

Parental  FPFCTIDPNESRVPVPDERFDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIF
          FPFCTIDPNESRVPVPDERFDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSH.SACDGIF
Retrocopy FPFCTIDPNESRVPVPDERFDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHFSACDGIF

Parental  -HLTRAFEDDDITHVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKLKPEYDIMCKVK
          .HLTRAFEDDDITHVE.SVDPIRDIEIIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKLKPEYDI.CKVK
Retrocopy <HLTRAFEDDDITHVEESVDPIRDIEIIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKLKPEYDITCKVK

Parental  SWVIDQKKPVRFYHDWNDKEIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALV
          SWVIDQKKPV.FYHDWNDKEIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALV
Retrocopy SWVIDQKKPVPFYHDWNDKEIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALV

Parental  IPFSGALELKLQELSAEERQKYLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQA
          IPFSGALELKLQELSAEERQ.YLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQA
Retrocopy IPFSGALELKLQELSAEERQQYLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQA

Parental  AGKIHTDFEKGFIMAEVMKYEDFKEEGSENAVKAAGKYRQQGRNYVVEDGDIIFFKFNTPQQPKKK
          AGKIHTDFEKGFIMAEV.KY.DFKEEGSENAVKAAGKYRQQGRNY.VEDGD.IFFKFNTPQQ.KKK
Retrocopy AGKIHTDFEKGFIMAEVVKYDDFKEEGSENAVKAAGKYRQQGRNYIVEDGDTIFFKFNTPQQLKKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1526 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006970	1 retrocopy	retro_btau_1737,
Choloepus hoffmanni	ENSCHOG00000005044	1 retrocopy	retro_chof_1295,
Callithrix jacchus	ENSCJAG00000007877	1 retrocopy	retro_cjac_2875,
Dipodomys ordii	ENSDORG00000008681	1 retrocopy	retro_dord_556,
Homo sapiens	ENSG00000138430	1 retrocopy	retro_hsap_2593,
Gorilla gorilla	ENSGGOG00000022215	1 retrocopy	retro_ggor_1623,
Myotis lucifugus	ENSMLUG00000025196	1 retrocopy	retro_mluc_626,
Monodelphis domestica	ENSMODG00000009296	1 retrocopy	retro_mdom_1428,
Nomascus leucogenys	ENSNLEG00000005817	1 retrocopy	retro_nleu_1526 ,
Otolemur garnettii	ENSOGAG00000016557	1 retrocopy	retro_ogar_1697,
Pongo abelii	ENSPPYG00000012943	2 retrocopies	retro_pabe_1912, retro_pabe_928,
Pan troglodytes	ENSPTRG00000012650	1 retrocopy	retro_ptro_1517,
Sorex araneus	ENSSARG00000010743	1 retrocopy	retro_sara_545,
Tarsius syrichta	ENSTSYG00000005517	2 retrocopies	retro_tsyr_1845, retro_tsyr_394,
Vicugna pacos	ENSVPAG00000009660	2 retrocopies	retro_vpac_52, retro_vpac_613,