RetrogeneDB ID: retro_nleu_463

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397265.1:20772048..20773754(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHQ1
• Ensembl ID: ENSNLEG00000002731
• Aliases: None
• Description: None

Sequence

>retro_nleu_463
ATGCTGACCCCGGCGTTCGACCTCAGCCAGAAGCCAGACTTTCTGACCATCCGCGTGCCCTCTGCCTGGGTCTCCGAGTT
CGACGTCTACTTCGAGGGGTCGGACTAGACTACCATGCCAAGCCGTACTTTCTCAGATTAACCCCTCCTGGAAGAATTGT
AGAAAATGGAAGCGAGCAAGGGTCCTATGATGCTATAAAGGAATTTTTACTATTCGCCTGCCCAAAGAAACCCCTGGCCA
GCATTTTGAGGGGCTGAACATGTGTTGCTCTTCTGGCACCAGGAAAATCCGCGACAGCAAAACCACTTGTGGAAGAAATA
GGTGATTCTGAGATTCCTGAGGAAGTAGATGAAGAGTTTGATTGGGAAATTGAGCAGACACCCTAGGAAGAGGTGATAGA
AAGTACTTTGAATCTTCAGTGCCGCTATGGGTTTGGAAACTTACGATCAAGAGTGTTTCAGCGGTTACAGGATGAATTGA
GTGATGTTATTAAGGATCCAGATTTCACCCCTGCAGCAGAACGAAAACAAAAGCACCTGGCCACTGAGCTGGCCAAGTTT
GATCCTGATCATTATCTAGCTGGCTTTTTTGAAGATGAGGCAGTTGAACAGATTTTGAAGTATAATCCTTGGTGGACTGA
CAAATATTAAAAAACGACAGCCTTTTTGGAAAAGAGTCAGAAGCAAGAAAATCATGATGCATTAGTGTCTTTTTCTGAAG
AAGAGAAATATCAGCTACAAGAATTTGTCAATAAATCTTATCTGCTAGACAAGAGAGCCTGTCGTCAAGTGTACTACAGT
TTGATTGATATCCTTCTGGCATATTGCTAAGAAACCCATGTCACTGAAGGAGAGAAGAACGTTGAATCTGCATGGAATAT
CAGGAAACTGAGTCCAATACTATGCTGGTTTGAGACTTGGACTAATGTTCATGATATCATGGTGTCTTTTGGAAGAAGGG
TATTGTGTTACCCACTGTATCGCCATTTCAAACTGGCGATGAAGGCCTACGGGGAGACTATAAAGATACTGCAACTACGT
AAAAGTGCAGTTTTAAAGTGTCTCCTGGATATTCACAAAATTTTTCAGGAAAACGACCTGGCATACATACTGAATGATCT
CTACATCTCAGACTACTGTGTGTGGATTCAGAAAGTCAAATCCAAAACGTTGGCAGTTCTTGCAGAAGCCTTAAAGGAAG
TCTCCCTTACAAAGGCCCAGTTGGGGTTAGAACTGGAAGAACTAGAAGCAGCAGCACTTCTTGTTCAGGAGGAAGAATCT
GCATTACAAGCAGCCCATTCAGTTTCTGGGCAGCAGAAACTTTGCTGCAGCTCTGAGGCAAGTGATTCGGAGGACTCAGA
CAGCACTGTGTCATCTGGAAACGAAGACTCAGACTCACATTCAGAACAAGATGAACTCAAAGATAGTCCATCTGAGACAG
TCAGTTCTTTGCAAGTTCCCCTTTTTGAAGAAAGCAGTGCCCTTCTTATTGTTGGTGGTGGAGTATGCAGAAACACAGCC
ATTCAGGAATCTGATGCCAGTCAGGGAAAGCCACTTGCCTCTTCCCGGCCTTTTGGAGTGTCTGGGCCTCTGATAGAGGA
GCTTGGGGAACAACTGAAGACCACAGTTCAGGTTTTTGAACCCAAGGGCACCACTGCTGTAAACCATAGCAATATGCAGG
AGAGAGATGGCTGTCAGACACCAAAT

Alignment

ORF - retro_nleu_463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.66 %
• Parental protein coverage: 99.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLTPAFDLSQDPDFLTIAIRVPYARVSEFDVYFEGSD-FKFYAKPYFLRLTLPGRIVENGSEQGSYDADK
          MLTPAFDLSQ.PDFLTI..RVP.A.VSEFDVYFEGSD.....AKPYFLRLT.PGRIVENGSEQGSYDA.K
Retrocopy MLTPAFDLSQKPDFLTI--RVPSAWVSEFDVYFEGSD<LDYHAKPYFLRLTPPGRIVENGSEQGSYDAIK

Parental  -GIFTIRL-PKETPGQHFEGLNMLTALLAPRKSRTAKPLVEEIGASEISEEVVDDEEFDWEIEQTPYEEV
          .GIFTIRL.PK........G.....ALLAP.KS.TAKPLVEEIG.SEI.EEV..DEEFDWEIEQTP.EEV
Retrocopy <GIFTIRL>PKKPLASILRG*TCV-ALLAPGKSATAKPLVEEIGDSEIPEEV--DEEFDWEIEQTP*EEV

Parental  SESALNPQCHYGFGNLRSGVLQRLQDELSDVIDIKDPDFTPAAERRQKRLAAELAKFDPDHYLADFFEDE
          .ES.LN.QC.YGFGNLRS.V.QRLQDELSDVI..KDPDFTPAAER.QK.LA.ELAKFDPDHYLA.FFEDE
Retrocopy IESTLNLQCRYGFGNLRSRVFQRLQDELSDVI--KDPDFTPAAERKQKHLATELAKFDPDHYLAGFFEDE

Parental  AIEQILKYNPWWTDKYSKMMAFLEKSQEQENHATLVSFSEEEKYQLRKFVNKSYLLDRRACRQVYYSLID
          A.EQILKYNPWWTDKY.K..AFLEKSQ.QENH..LVSFSEEEKYQL..FVNKSYLLD.RACRQVYYSLID
Retrocopy AVEQILKYNPWWTDKY*KTTAFLEKSQKQENHDALVSFSEEEKYQLQEFVNKSYLLDKRACRQVYYSLID

Parental  ILLAYCYETRVTEGEKNVESAWNIRKLSPTLCWFETWTNVHDIMVSFGRRVLCYPLYRHFKLVMKAYRDT
          ILLAYC.ET.VTEGEKNVESAWNIRKLSP.LCWFETWTNVHDIMVSFGRRVLCYPLYRHFKL.MKAY..T
Retrocopy ILLAYC*ETHVTEGEKNVESAWNIRKLSPILCWFETWTNVHDIMVSFGRRVLCYPLYRHFKLAMKAYGET

Parental  IKILQLGKSAVLKCLLDIHKIFQENDPAYILNDLYISDYCVWIQKVKSKKLAALAEALKEVSLTKAQLGL
          IKILQL.KSAVLKCLLDIHKIFQEND.AYILNDLYISDYCVWIQKVKSK.LA.LAEALKEVSLTKAQLGL
Retrocopy IKILQLRKSAVLKCLLDIHKIFQENDLAYILNDLYISDYCVWIQKVKSKTLAVLAEALKEVSLTKAQLGL

Parental  ELEELEAAALLVQEEETALKAAHSVSGQQTPCSSSGASDSEDSDSTVSSGKEDSDSDSEQDELKDSPSET
          ELEELEAAALLVQEEE.AL.AAHSVSGQQ..C.SS.ASDSEDSDSTVSSG.EDSDS.SEQDELKDSPSET
Retrocopy ELEELEAAALLVQEEESALQAAHSVSGQQKLCCSSEASDSEDSDSTVSSGNEDSDSHSEQDELKDSPSET

Parental  VNSLQGPFLEESSALLIVDGGVRRNTAIQESDASQGKPLASSRPLGVSGPLIEELGEQLKTTVQVSEPKG
          V.SLQ.P..EESSALLIV.GGV.RNTAIQESDASQGKPLASSRP.GVSGPLIEELGEQLKTTVQV.EPKG
Retrocopy VSSLQVPLFEESSALLIVGGGVCRNTAIQESDASQGKPLASSRPFGVSGPLIEELGEQLKTTVQVFEPKG

Parental  TTAVNHSNMQKRDGCQTPN
          TTAVNHSNMQ.RDGCQTPN
Retrocopy TTAVNHSNMQERDGCQTPN

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_463 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015131	1 retrocopy	retro_cjac_1045,
Homo sapiens	ENSG00000144736	1 retrocopy	retro_hsap_674,
Gorilla gorilla	ENSGGOG00000034818	1 retrocopy	retro_ggor_581,
Nomascus leucogenys	ENSNLEG00000002731	1 retrocopy	retro_nleu_463 ,
Pongo abelii	ENSPPYG00000013717	1 retrocopy	retro_pabe_546,
Pan troglodytes	ENSPTRG00000015106	1 retrocopy	retro_ptro_486,