RetrogeneDB ID: retro_nleu_1999

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397321.1:9478073..9479235(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS31
• Ensembl ID: ENSNLEG00000001164
• Aliases: None
• Description: None

Sequence

>retro_nleu_1999
ATGTTTCCTAGACTCTCGACGTTCCTATCTCTTTGCCCCTTTTCCCGCCACCCTTTGTCCTCCGGAAGCCCGGAGACATC
AGCCGCTGCGATTGTGCTACTGGCTGTTCGGCACAGAACGGTCAAGATAAAAAATAAATCCAAAGATATTTTGGCACTAA
CAGCGTGATCTGTAGCAAGAAAGATGAGCAGTTTGTTCAAACCGATGAGACTTCCAAGGAGACTTCAGAGAGCCAAGACA
GTGAAAAGGAAAATATGAGAAAGACTTGTTAAACATTATTAAGGGCATGAAAGTTGGATTAAGCACAGTAAATGTACAAA
CAACAAAGCCCCCCAACAGAAGACCACTTAAAAGTTTGGAAGCTACACTTGGCAGACCTCAAAGAGCTACAGAACATGCT
CCGAAGAAGAGAATTGGAGCCCCTGAGTCTTGAGTTGGTGGCAGCTGCATCTGGTGTGGCAGATTCTCTCTCTTTTGACA
AGCAAACAACCAAGTCGGAGCTGCTGAGGCAGCTCCAGCAGCATTAGGAAGAGTCAAGGGCACAGAGAGATGCAGAGAGA
CCTAAAATTAGTTTCAGTAACATAATATAGATAAGAAAGTTGCCAGGTTTGCTACAGCTAGAGTTCGTTCAAGACCAGAG
CATCGGATTCAGTTTGACGAAGCCTATGACAATTATCCTGGCCAGGAGAAGACCTATGATCATAGAAAAAGATGTAGGAA
AGATATATTCAAGTGGAAAAGACTTAATATTTTTGACATGACGGCAGTTACTAAACAAGCACCTGAAACAGACACATCAC
CTTCACTTTGGGATGTGGAATTTGCTAAGCAGTTAGCCACAGTAAATGAACAACCCCTTCAGAATGGGTTTGAAAAGCTG
ATCCAGTGGACAAAAGAGGGGAAATTGTGGGAGTTCCCAATTAACAATGAAGCAGGTTTTGATGATGATGGTTCAGCATT
TCATGAACATATATTTCTGGAGAAACACCTGAAGGGCTTTCCAAAACAAGGACCAATTCACCACTTCATGGAGGTGATGA
CTTGTCGCCTTTCCAAAAACTCATGTCTTAGTGTTAAACAGAATGTTGAGCACATAGAGTGGTTTAGAAATTATTTTAAT
GAAAAAAAGGACGTTCTAAAAGAAAGTAATGTACAGTTCAAT

Alignment

ORF - retro_nleu_1999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MFPRVSTFLPLRPFSRHPSSSGSPETSAAAIMLLAVRHGTVRTKNN-IQRYFGTNSVICSKKDKQSVRTD
          MFPR.STFL.L.PFSRHP.SSGSPETSAAAI.LLAVRH.TV..KN..IQRYFGTNSVICSKKD.Q.V.TD
Retrocopy MFPRLSTFLSLCPFSRHPLSSGSPETSAAAIVLLAVRHRTVKIKNK<IQRYFGTNSVICSKKDEQFVQTD

Parental  ETSKETSESQDSEKENTKK-DLLGIIKGMKVELSTVNVRTTKPPKRRPLKSLEATLGRLQRATAYAPKKR
          ETSKETSESQDSEKEN..K.DLL.IIKGMKV.LSTVNV.TTKPP.RRPLKSLEATLGR.QRAT..APKKR
Retrocopy ETSKETSESQDSEKENMRK<DLLNIIKGMKVGLSTVNVQTTKPPNRRPLKSLEATLGRPQRATEHAPKKR

Parental  I-EPLSPELVAAASAVADSLPFDKQTTKSELLSQLQQHEEESRAQRDAERPKISFSNII-SDMKVARSAT
          I.EPLS.ELVAAAS.VADSL.FDKQTTKSELL.QLQQH.EESRAQRDAERPKISFSNII..D.KVAR.AT
Retrocopy I>EPLSLELVAAASGVADSLSFDKQTTKSELLRQLQQH*EESRAQRDAERPKISFSNII<IDKKVARFAT

Parental  ARVRSRPELQIQFDEGYDNYPGQEKTDDLRKR--KNIFTGKRLNIFDMMAVTKEAPETDTSPSLWDVEFA
          ARVRSRPE..IQFDE.YDNYPGQEKT.D.RKR..K.IF..KRLNIFDM.AVTK.APETDTSPSLWDVEFA
Retrocopy ARVRSRPEHRIQFDEAYDNYPGQEKTYDHRKRCRKDIFKWKRLNIFDMTAVTKQAPETDTSPSLWDVEFA

Parental  KQLATVNEQPLQNGFEELIQWTKEGKLWEFPINNEAGFDDDGSEFHEHIFLEKHLESFPKQGPIRHFMEL
          KQLATVNEQPLQNGFE.LIQWTKEGKLWEFPINNEAGFDDDGS.FHEHIFLEKHL..FPKQGPI.HFME.
Retrocopy KQLATVNEQPLQNGFEKLIQWTKEGKLWEFPINNEAGFDDDGSAFHEHIFLEKHLKGFPKQGPIHHFMEV

Parental  VTCGLSKNPYLSVKQKVEHIEWFRNYFNEKKDILKESNIQFN
          .TC.LSKN..LSVKQ.VEHIEWFRNYFNEKKD.LKESN.QFN
Retrocopy MTCRLSKNSCLSVKQNVEHIEWFRNYFNEKKDVLKESNVQFN

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_1999 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008470	1 retrocopy	retro_chof_586,
Equus caballus	ENSECAG00000003600	1 retrocopy	retro_ecab_1028,
Nomascus leucogenys	ENSNLEG00000001164	1 retrocopy	retro_nleu_1999 ,
Oryctolagus cuniculus	ENSOCUG00000021467	1 retrocopy	retro_ocun_1747,
Otolemur garnettii	ENSOGAG00000024374	1 retrocopy	retro_ogar_914,
Ochotona princeps	ENSOPRG00000014606	1 retrocopy	retro_opri_1137,
Pongo abelii	ENSPPYG00000005306	1 retrocopy	retro_pabe_3785,
Sorex araneus	ENSSARG00000004428	1 retrocopy	retro_sara_594,
Sarcophilus harrisii	ENSSHAG00000007140	1 retrocopy	retro_shar_591,
Tarsius syrichta	ENSTSYG00000002170	1 retrocopy	retro_tsyr_238,
Tursiops truncatus	ENSTTRG00000012556	1 retrocopy	retro_ttru_1285,