RetrogeneDB ID: retro_nleu_2060

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397325.1:9577230..9577896(-)
• 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_2060
CACATCATGTGGGAAGCTGGCCGGCTAGGACCCAAGGTGAACAAGAAGGAAGTGGTAGAGGCTATGACCATTGTGGAGAC
ACTGCCCATGGTGGTTGTAGGCATCCTGGGCTATATGGAAACCCCTCAAGGCCTCTGAATTTCCAAGACCATCTTTGTTG
AGCACAGTAGCAATGAGTGCAAAAGGCACTTCTATAGGAACTGGCATAAAGCTAAGTAGAAGGCCTTTACCAAGTACTGC
AAGAAATGGCAGGGTGAGGATGACAAGAAGCAGCTGAAGAAGGACTTCAACAGCATGAAAAAGTACTGCCAAGTCATCCA
CATCAATATCTACACCCAGATGCACCTGCTTCCTCTGTGTCTGAAGAAGACCCACCTCATGGAGATCCAGGTGAACAGAG
GCACTGTGATCGAGAAACCGGACTGGTCCCTGGAGAGGCTAGAGGACCAGGTACCTGTGAAACAAGTGTTTGGGCAGGAC
AAGATGATTGACATCAAACGGGTGACCAAGGGCAAAAGCTACAAAGAGGTCACCAGTCATTGGCATACCAAGAAGCTGCC
CTACAAGACCCACTGAGGGCTGTACAAGGTTGCCTATATTGGGGCATGGCATCCTGCCCATATGACCTTCTCTGTGGCAT
GTACTGGACACAAACCATCACTGCAC

Alignment

ORF - retro_nleu_2060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.46 %
• Parental protein coverage: 54.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HTLREVHRPGLKISKREEVEAVTIVETPPVVVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHK
          H...E..R.G.K..K.E.VEA.TIVET.P.VVVG..GY..TP.GL...KTIF.EH.S.EC.R.FY..WHK
Retrocopy HIMWEAGRLGPKVNKKEVVEAMTIVETLPMVVVGILGYMETPQGL*ISKTIFVEHSSNECKRHFYRNWHK

Parental  SKKKAFTKACKRWRDTDGKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKV
          .K.KAFTK.CK.W...D.KKQL.KDF..MKKYC.VI.....TQM.LLP...KK.H.MEIQ.N.GTV.EK.
Retrocopy AK*KAFTKYCKKWQGEDDKKQLKKDFNSMKKYCQVIHINIYTQMHLLPLCLKKTHLMEIQVNRGTVIEKP

Parental  AWAQARLEKQVPVHSVFSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGC
          .W...RLE.QVPV..VF.Q...ID...VTKG...K.VTS.WHTKKLP.KTH.GL.KVA.IGAWHPA....
Retrocopy DWSLERLEDQVPVKQVFGQDKMIDIKRVTKGKSYKEVTSHWHTKKLPYKTH*GLYKVAYIGAWHPAHMTF

Parental  SIARAGQKGYHH
          S.A..G.K...H
Retrocopy SVACTGHKPSLH

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_2060 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,