RetrogeneDB ID: retro_nleu_1249

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397286.1:17998652..17999831(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3L
• Ensembl ID: ENSNLEG00000008850
• Aliases: None
• Description: None

Sequence

>retro_nleu_1249
ATATCTCACTGAAAGTTCTCCGCTCCCAGACACGGGTCCCTCGGCTTCCTGCCTTGAAAGCGCGGCTGCAGGCATTGTGG
GAAGGTGGAGAGTTTCCCTAAGGATGACCCTTCCAAGCTGGTCCACCTCACAGCCTTCTTGAGATACAAGGTTGGCATGA
CCCACATCGTGAGGGGAAGTCAACAGGCCAGGATCCAAGATGAATATGAAGGAGGTGGTAGAGGCTGTGGCCATTGTGGA
GACAACCACCCATGGTGGTTGTGAGCATTGTGGGATATGGGGAAACCCTTCGAGGCATCTGGAATTTCAAGACCATTTTT
GCTGAGCACATCAGCAATGAGTGCAAAAGGCGTTTCTATAAGAACTGACATAAATCTAAGAAGAAGCCCTTTACCAAGTA
CTGCAAGAAATGGCAGAAAAGATGGCAAAAAGCAGGTGTAGAAGGACTTCAGCAGCATGAAGAAGTACTGCCAGGTCATC
CGTGTCATTGCCCACACCCAGATGCACCTGCGTCCTCTGCACCAGAAAGCCCACCTGATGGAGATCTAGGTGAATCAAGA
CACTGTGGCCGAAACGCTGGACTGGGCCTAGAAGAGGCTCGAGCAGCAGGTGCCTGTGAACCAAGTGTTTGAGCAGGATG
AGATGATCAAAGTCATCGGGGTGACAAAGGGCAAAGGCTACAAAGGGGTCACCAGTTGTTGGCACACCAAGAAGCTGCCC
CACAAGACCCACCGAGGCTTGTGCAAGGTGGCCTGTATTGGGACATGGCATCTTGCCCATGTGGCCTTCTCTGTGGCACG
CACTGGCCAGAAAGGCTACCATCATGGCACTGAGATCAACAAGAAGATCTATAAGATCGGCCAGGGCTACCCTATCACGG
ACGGCAAACTGATCAAGAACAATGCCTCCATTGACTATGACCTGTCTGACAAGAGCATCAACCCTCTGGGTGGCTTTGTC
CACTGTGGCAAAGTGACCAATGACTTTGTCATGCTGAAAGGCTATGTGGTGGGAACCAAGAAGCAAGTGCTCACCCTCTG
CAAGTCCTTGCTGGTCCAGACCAAATGGCAGGCTCTGGAGAAGATTGACCTTAAGTTCATTGACACCACCTCCAAGTTTG
GCCATTGCCACTTCCAGACCATGGAGGAGAAGAAAGCATTCATGAGACCACTCAGGAAA

Alignment

ORF - retro_nleu_1249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.83 %
• Parental protein coverage: 96.81 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGHLGFLPHKRSRRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLR-EVHRPGLKISK
          .SH.KFSAPRHG.LGFLP.KR..RH.GKV...P.DDPS..VHLTAFL.YK.GMTH..R.EV.RPG.K...
Retrocopy ISH*KFSAPRHGSLGFLP*KRGCRHCGKVESFPKDDPSKLVHLTAFLRYKVGMTHIVR>EVNRPGSKMNM

Parental  REEVEAVTIVET-PPVVVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWR
          .E.VEAV.IVET.PP.VVV..VGY..T.RG...FKTIFAEH.S.EC.RRFYK..HKSKKK.FTK.CK.W.
Retrocopy KEVVEAVAIVET>PPMVVVSIVGYGETLRGIWNFKTIFAEHISNECKRRFYKN*HKSKKKPFTKYCKKWQ

Parental  -DTDGKKQLQKDFAA-MKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVP
          .....K.......AA.MKKYC.VIRVI.HTQM.L.P..Q.KAH.MEI..N..TVAE...WA..RLE.QVP
Retrocopy <EKMAKSRCRRTSAA<MKKYCQVIRVIAHTQMHLRPLHQ-KAHLMEI*VNQDTVAETLDWA*KRLEQQVP

Parental  VHSVFSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHH
          V..VF.Q.E.I.VI.VTKG.G.KGVTS.WHTKKLP.KTH.GL.KVACIG.WH.A.V..S.AR.GQKGYHH
Retrocopy VNQVFEQDEMIKVIGVTKGKGYKGVTSCWHTKKLPHKTHRGLCKVACIGTWHLAHVAFSVARTGQKGYHH

Parental  RTELNKKIYRIGRGPHMEDGKLVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRVIT
          .TE.NKKIY.IG.G....DGKL.KNNAS..YD...KSI.PLGGF.H.G.V.NDFVMLKG...GTKK.V.T
Retrocopy GTEINKKIYKIGQGYPITDGKLIKNNASIDYDLSDKSINPLGGFVHCGKVTNDFVMLKGYVVGTKKQVLT

Parental  LRKSLLVHHSRQAVENIELKFIDTTSKFGHGRFQTAQEKRAFMGPQKK
          L.KSLLV....QA.E.I.LKFIDTTSKFGH..FQT..EK.AFM.P..K
Retrocopy LCKSLLVQTKWQALEKIDLKFIDTTSKFGHCHFQTMEEKKAFMRPLRK

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_1249 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 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008489	1 retrocopy	retro_amel_1881,
Nomascus leucogenys	ENSNLEG00000008850	9 retrocopies	retro_nleu_1107, retro_nleu_1130, retro_nleu_1249 , retro_nleu_1305, retro_nleu_1673, retro_nleu_1824, retro_nleu_2046, retro_nleu_2060, retro_nleu_3126,
Nomascus leucogenys	ENSNLEG00000015234	2 retrocopies	retro_nleu_1038, retro_nleu_1449,
Pongo abelii	ENSPPYG00000006973	1 retrocopy	retro_pabe_2854,
Pan troglodytes	ENSPTRG00000007617	12 retrocopies	retro_ptro_1439, retro_ptro_1473, retro_ptro_1753, retro_ptro_2150, retro_ptro_2339, retro_ptro_2462, retro_ptro_2501, retro_ptro_2646, retro_ptro_2741, retro_ptro_2767, retro_ptro_3163, retro_ptro_916,
Ictidomys tridecemlineatus	ENSSTOG00000012921	2 retrocopies	retro_itri_1344, retro_itri_867,