RetrogeneDB ID: retro_nleu_2046

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397324.1:7623676..7624831(-)
• 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_2046
CCCAGACACGGGTCCCTCGGCTTCCTGCCTCAGAAGTGCAGCAGGAGACATCACAGGAAGGTGAAGAGCTTCCCTAAAGA
TGACCCTTCCAAGGCGGTCCACCTCACAGCCTCCCTGGGATACAAGGCTGGCATGACCCACATCGTGCGGGAAGTCGACA
GGCCAGGATCCAAGGTGAACAAGAAGGAGGTGGTGGAGGCTGTGACCATTGTGGAGACAACTATGGTGGTTGTGGGCAAT
GTGGGCTATGTGGGAACCCCTCGAGGCCTCTGGACCTTCAAGAACGTCTTCGCTGAGCACATCAGTGATGAGTGCAAGAG
GCACTTCTATAAGAACTGGCATAAATCTAAGAAGAAGGCCTTCACCAAGTACTGCAAGAAATGGCGGGATGAGGATAGCA
AGAAGCAGCTGGAGAAGGACTTCAGCACCATGAAGAAGTACTGCCAAGTCATCCATATCATTACCCACAACCAGATGCGC
CTGCTTCTTCTGCTCCACAAGAAGGCCCACCTGATGGAGATCCAGGTAAACGGAGGCACTGTGGCTGAGAAGCTGGACTG
GGCCCGTGAGAGGCTTGAGCAGCAGGTACCTGTGAACCAGGTGTTTGGGCAGGATGAGATGATTGATGTCATTGGGGTGA
CAAAGAGCAAAGGCTACCAAGGGGTCACCAGTCATTGGCACACCAAGAAGCTGTCCTGCAAGATCCGCTGAGGCCTCTGC
AAGGTGGCCTGTATTGGGGCATGGCATCCTGCCTGTGTGGCCTTCTCTGGGGCACGCACTGGGCAGAAAGAGTACCATCA
CTGCACTGAGATCAACAAGAAGATCTATAAGATCGACCAGAGCTACCTTATCAAGGGTGGCAAACTGATCAAGAACAATG
CCTCCACTGACTATGACCTGTCTGTCAAGAGCATCAACCCTCTGGGTGGCTTTGTCCACTATGGTGAAGTGACCAATGAC
TTTGTCATGCTGAAAGGCCGTGTGGTTGTAACCAAGAAGCGAGTGCTCACCCTCCGCAAGTCCTTGCTGGTGCAGACCAA
ATGACAGGCTCTGGAGAAGACTGACCTTAAGTTCATTGACACCACCTCCACGTTTGGCCATGACTGCTTCCAGACCATGG
AGGAGAAGAAAGCATTCGTGGGAGCACTCAAGAAA

Alignment

ORF - retro_nleu_2046 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.1 %
• Parental protein coverage: 94.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRHGHLGFLPHKRSRRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKREEVEAVTI
          PRHG.LGFLP.K.SRRH..KVK..P.DDPS..VHLTA.LGYKAGMTH..REV.RPG.K..K.E.VEAVTI
Retrocopy PRHGSLGFLPQKCSRRHHRKVKSFPKDDPSKAVHLTASLGYKAGMTHIVREVDRPGSKVNKKEVVEAVTI

Parental  VETPPVVVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWRDTDGKKQLQK
          VET...V.........TPRGL..FK..FAEH.SDEC.R.FYK.WHKSKKKAFTK.CK.WRD.D.KKQL.K
Retrocopy VETT-MVXXXXXXXXXTPRGLWTFKNVFAEHISDECKRHFYKNWHKSKKKAFTKYCKKWRDEDSKKQLEK

Parental  DFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHSVFSQSEVID
          DF..MKKYC.VI..I.H.QM.LL....KKAH.MEIQ.NGGTVAEK..WA..RLE.QVPV..VF.Q.E.ID
Retrocopy DFSTMKKYCQVIHIITHNQMRLLLLLHKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMID

Parental  VIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTELNKKIYRIG
          VI.VTK..G..GVTS.WHTKKL..K...GL.KVACIGAWHPA.V..S.AR.GQK.YHH.TE.NKKIY.I.
Retrocopy VIGVTKSKGYQGVTSHWHTKKLSCKIR*GLCKVACIGAWHPACVAFSGARTGQKEYHHCTEINKKIYKID

Parental  RGPHMEDGKLVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRVITLRKSLLVHHSRQ
          .......GKL.KNNAST.YD...KSI.PLGGF.HYGEV.NDFVMLKG....TKKRV.TLRKSLLV....Q
Retrocopy QSYLIKGGKLIKNNASTDYDLSVKSINPLGGFVHYGEVTNDFVMLKGRVVVTKKRVLTLRKSLLVQTK*Q

Parental  AVENIELKFIDTTSKFGHGRFQTAQEKRAFMGPQKK
          A.E...LKFIDTTS.FGH..FQT..EK.AF.G..KK
Retrocopy ALEKTDLKFIDTTSTFGHDCFQTMEEKKAFVGALKK

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_2046 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,