RetrogeneDB ID: retro_nleu_49

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397347.1:1310692..1311901(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018823
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TFDP1
• Ensembl ID: ENSNLEG00000000849
• Aliases: None
• Description: None

Sequence

>retro_nleu_49
ATGGCAAAATATGTCAGTCTAACCGAAGCTAACGAAGAACTCAAGGTCTTAACAGACCAGAACCAGACCAGTGGCCCCGT
GGCCGTTTACCTCTCCACCGTGAACCCGCTCGGGAAGCAGCTCTTGCCGCAAACCTTTGGACAGTCCAATGTCAACATTG
ACCAGCAAGTGTTAATTGTTATGCTTCAGAGACCGGCAGCATCAAACATCCTTGTGGTAGGAAGCCCAAACCCACCCAGC
ACTCACTTTGCCTCTCAGAACCAGCCTTCCTACTTCTCACTTCCGTGGGCCGGGCAGCACAACAGGAAAGGAGAGAAGAA
TGTCATGGGCCTGTGCCATGTTTCCATGAAGGTCTGGGAGATGGTGCAGAGGAAAGGGACCACTTCCTGCCAGGAAGTGT
TGGGTGAGCTGATCGCCGAGTTCAGAGCTGCCAGCAGCCACGTCTCACCAAACAGGTCAGCTGGTGACGTGGAGAACATA
AAACGGCGCACCTACGATGCCTTAAACGTGCTGATGGCCATGAATATCATCTCCAGGGAGAAAAACAAAATCAAGTGGAT
TGGTCTGACCACCAACTCGGCTCAGAACTGTCAGAACTTACGGGTGGAAAGACAGAAGAGACTTGAAAGAATAAAGCAGA
AACAGTCTGAACTTCAACAACTTATTCTACAGCAAATTGCCTTGAAGAACCTGGTGCTGAGAAACCAGTATGTGGAGAAG
CAGGTCGGCCAGCAGCCGCCACCCAACTCAGTCATCCACTTGCCCTTCATCATCATCAGCACTAGCAAGAAGACCGTCAT
TAACTGCAGAGTCTCCAACAACAAATCAGATTATCTGTTTAATTTTAACGGCCCATTCGAAATCCACAATGACACAGAAG
TGCTGATGTGGATGGGCATGGCTTTTGGGCTAGAGTCCGGGAGCTGCTCTGCCGAAGACCTTAAAATGGCCAAAAGTTTG
GTCCCAAAGGCTCTGGAGCCGTACGTGACAGAAATGGCTCAGGGAACTTTTGGAGGTGTATTCACGACGGCAGGTTCCAC
GTCTAATGGCACGTGGCCTTCTGCCAGTGACCTGACCAACAGTGCGGATGGGATGCTGGCCACAAGCTCCAATGGGTCTC
AGTACAGTGGCTCCAGGGTGGAGACCGCAGCAGTCGAGGAGGAGGAGGACAACAACGATGACGACTTCAATGAGAATGAC
AAGGATGAC

Alignment

ORF - retro_nleu_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.05 %
• Parental protein coverage: 92.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAVHPSTVNPLGKQLLPKTFGQSNVNIAQQVVIGTPQRPAASNTLVVGSPHTPSTHFASQNQPSDSS-PW
          VAV..STVNPLGKQLLP.TFGQSNVNI.QQV.I...QRPAASN.LVVGSP..PSTHFASQNQPS..S.PW
Retrocopy VAVYLSTVNPLGKQLLPQTFGQSNVNIDQQVLIVMLQRPAASNILVVGSPNPPSTHFASQNQPSYFSLPW

Parental  SAGKRNRKGEKNGKGR-HFSMKVCEKVQRKGTTSYNEVADELVAEFSAADNHILPNESAYDQKNIRRRVY
          .AG..NRKGEKN..G..H.SMKV.E.VQRKGTTS..EV..EL.AEF.AA..H..PN.SA.D..NI.RR.Y
Retrocopy -AGQHNRKGEKNVMGLCHVSMKVWEMVQRKGTTSCQEVLGELIAEFRAASSHVSPNRSAGDVENIKRRTY

Parental  DALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEVERQRRLERIKQKQSQLQELILQQIAFKNLVQRN
          DALNVLMAMNIIS.EK..IKWIGL.TNSAQ.CQNL.VERQ.RLERIKQKQS.LQ.LILQQIA.KNLV.RN
Retrocopy DALNVLMAMNIISREKNKIKWIGLTTNSAQNCQNLRVERQKRLERIKQKQSELQQLILQQIALKNLVLRN

Parental  RHAEQQASRPPPPNSVIHLPFIIVNTSKKTVIDCSISNDKFEYLFNFDNTFEIHDDIEVLKRMGMACGLE
          ...E.Q....PPPNSVIHLPFII..TSKKTVI.C..SN.K..YLFNF...FEIH.D.EVL..MGMA.GLE
Retrocopy QYVEKQVGQQPPPNSVIHLPFIIISTSKKTVINCRVSNNKSDYLFNFNGPFEIHNDTEVLMWMGMAFGLE

Parental  SGSCSAEDLKMARSLVPKALEPYVTEMAQGTVGGVFITTAGSTSNGTRFSASDLTNGADGMLATSSNGSQ
          SGSCSAEDLKMA.SLVPKALEPYVTEMAQGT.GGVF.TTAGSTSNGT..SASDLTN.ADGMLATSSNGSQ
Retrocopy SGSCSAEDLKMAKSLVPKALEPYVTEMAQGTFGGVF-TTAGSTSNGTWPSASDLTNSADGMLATSSNGSQ

Parental  YSGSRVETPVSYVGEDDEEDDDFNENDEDD
          YSGSRVET......E.D..DDDFNEND.DD
Retrocopy YSGSRVET-AAVEEEEDNNDDDFNENDKDD

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_49 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 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004467	8 retrocopies	retro_chof_2187, retro_chof_2229, retro_chof_2621, retro_chof_506, retro_chof_529, retro_chof_837, retro_chof_854, retro_chof_895,
Callithrix jacchus	ENSCJAG00000006950	2 retrocopies	retro_cjac_179, retro_cjac_4094,
Homo sapiens	ENSG00000198176	4 retrocopies	retro_hsap_1601, retro_hsap_299, retro_hsap_4803, retro_hsap_61,
Gorilla gorilla	ENSGGOG00000004908	2 retrocopies	retro_ggor_17, retro_ggor_335,
Loxodonta africana	ENSLAFG00000007927	1 retrocopy	retro_lafr_914,
Myotis lucifugus	ENSMLUG00000012165	1 retrocopy	retro_mluc_896,
Macaca mulatta	ENSMMUG00000007423	1 retrocopy	retro_mmul_177,
Mus musculus	ENSMUSG00000038482	2 retrocopies	retro_mmus_3243, retro_mmus_338,
Nomascus leucogenys	ENSNLEG00000000849	3 retrocopies	retro_nleu_2177, retro_nleu_2598, retro_nleu_49 ,
Otolemur garnettii	ENSOGAG00000003532	1 retrocopy	retro_ogar_3334,
Pongo abelii	ENSPPYG00000025889	3 retrocopies	retro_pabe_1314, retro_pabe_132, retro_pabe_378,