RetrogeneDB ID: retro_nleu_1824

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397312.1:7817550..7818597(+)
• 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_1824
ATGTCTCACAGAAAGGTCTCCGCTCCCAGACATGGGTCCCTCAGCTTCCTGCCCCAGAAGCGCAGCAGCAGGCATTGTGG
GAAGGTGAGGAGCCTCCCTAAGGATGACCCTTCCAAGCCAGTCTGCCTCACAGGCTTCCTGGGATACAAGGCTGGCATGA
CCCACATCATGCAGGAAGTCAACAGGCCAGGATCCAAGGTGAATAAGAAGGAGGTGGTAGAGGCTGTGACCATTGTAGAG
ACACCACCCATGATGGTTGTGGGCATTGTGGGCTATGTGGAAACCCCTCAAGGCCTCCAGACCTTCAAGACCGTCTTCGC
TGAGCACATCAGTGATAAGTGCAAGAGGCACTTCTATAAGAACTGGCATAAATCTAAGAAGGCCTTTACCAAGTACTGCA
AGAAATGGCAGGATGAGAATGGCAAGAAGCAGCTGGAGAAGGACTTCAGCAACATGAAGAAGTACTGCCAAGTCATCCAC
ATCATTGCTCACACCTAGATGTGCCTGCTTCCTCTGCGCCAGAAGAAGGCCCACCTGCTGGAGATCCAGGTGAATGGAGA
CACCATGGCTGAGAAGCTGGACTGGGCCCGCGAGAGGTTTGAGCAGCAGTTACCTGTGAACCATGTGTTTGGGCAGGACA
AGATGATTGACGTCATCAGAATGACAAAGGGCAAAGGCTACAAGGGGGTCACCAGTCGTTGGCACACCAAGAAGCTGCCC
CGCAAGACCCAGCAAGGCCTGCGCAAGGTGTCCTGTATTAGGGCATGGCATCTTGTCCGTGTAGCCTTCTCTGTGGCACA
TGCTTGGCAAAAAGGCCACCGTCACCACACTGAGATCAATAAGAAGATCTACAAGATTGGCCAGGGCTACCTTATCAAGG
ATGACAAACTGATCAAGAACAATGCCTCCACTGACTATGACCTGTCTGACAAGAGCATCAACCCTCTGGGTGGCTTTGGC
CACTATGGTGAAGTGACCAATGACTTTGTCATGCTGAAGGGCTGTGTGCTAGGAACCAAGAAGCGAGTGCTCACCCTCCC
CGCAAGT

Alignment

ORF - retro_nleu_1824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.14 %
• Parental protein coverage: 86. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGHLGFLPHKRSRRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKR
          MSHRK.SAPRHG.L.FLP.KRS.RH.GKV...P.DDPS.PV.LT.FLGYKAGMTH...EV.RPG.K..K.
Retrocopy MSHRKVSAPRHGSLSFLPQKRSSRHCGKVRSLPKDDPSKPVCLTGFLGYKAGMTHIMQEVNRPGSKVNKK

Parental  EEVEAVTIVETPPVVVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWRDT
          E.VEAVTIVETPP..VVG.VGYV.TP.GL..FKT.FAEH.SD.C.R.FYK.WHKSKK.AFTK.CK.W.D.
Retrocopy EVVEAVTIVETPPMMVVGIVGYVETPQGLQTFKTVFAEHISDKCKRHFYKNWHKSKK-AFTKYCKKWQDE

Parental  DGKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHSV
          .GKKQL.KDF..MKKYC.VI..I.HT.M.LLP.RQKKAH..EIQ.NG.T.AEK..WA..R.E.Q.PV..V
Retrocopy NGKKQLEKDFSNMKKYCQVIHIIAHT*MCLLPLRQKKAHLLEIQVNGDTMAEKLDWARERFEQQLPVNHV

Parental  FSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTEL
          F.Q...IDVI..TKG.G.KGVTSRWHTKKLPRKT..GLRKV.CI.AWH..RV..S.A.A.QKG..H.TE.
Retrocopy FGQDKMIDVIRMTKGKGYKGVTSRWHTKKLPRKTQQGLRKVSCIRAWHLVRVAFSVAHAWQKGHRHHTEI

Parental  NKKIYRIGRGPHMEDGKLVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRVITLRKS
          NKKIY.IG.G....D.KL.KNNAST.YD...KSI.PLGGF.HYGEV.NDFVMLKGC..GTKKRV.TL..S
Retrocopy NKKIYKIGQGYLIKDDKLIKNNASTDYDLSDKSINPLGGFGHYGEVTNDFVMLKGCVLGTKKRVLTLPAS

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_1824 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,