RetrogeneDB ID: retro_nleu_1198

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397284.1:7257874..7258852(-)
• Located in intron of: ENSNLEG00000002937

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM175A
• Ensembl ID: ENSNLEG00000009133
• Aliases: None
• Description: None

Sequence

>retro_nleu_1198
AATTCCTCAAGTGAAATAAATGAGCAAGCACTGCAGAAAATATTCTCCAATGTCAAAAAGAATGTGATAGGTTGGTACAA
ATTCCGTCATCATTCAGATCAGATCATGATGTTTAGAGAGAGGCTGCTTCACAAAAACTTGCAGGAGCAGTTTTCAAACC
AAGAACTTGTTTTTCTACTATTAACACCAAGTATAATAACAGAAAGCTGCTCTACTCATCGACTGAAACATGCCTTGAAA
CCTCAAAAAGGACTTTTTCACAGGGTACCTTTAGTGGTTGCCAATCTGGGTATTTCTGAACAACTAGGTTATAAAACTGT
ATCAGGTTCCTGTATGTCCACTGGTTTTAGCCAAGCAGTAAAAACACACAGCTCTAAATTTTTTGAAGAAGATGGATCAT
TAAAGGAGGTACATAAGATAAATGAAATATAATGCTTCATTACAAGAGGAATTAAAGAGTATATGCAAAAAAAAGTGGAA
GACAATGAACAAGCAATAAATAAACTAGTAAAGGATATAAACAGATTAAAACAAGAAATTGGAAAAAAGGATATGACCGT
AGATTCAGGCAGCATGAGAGAAAAACATCTAAAAAGACCCTCAGGGGAACATTTTTCCTCGTCAAGCATTATGGACCTTT
TATCCAGATTCTGAATTTCTTCATTCATGTGTTATGTCTTTAAAAAACAGACATGTTTCTAAAAGCTGTAACAACAACCT
CCACCTCGATGTAGTAGCCAATCTGACCTTAATGATAGAACACACTGACATTCCTGAAGCTACTCTAGCTAGTAGACCAC
AAATGATTAAGCATAAAGCCTTAGACTTAGATGACGATTCAAGAGATCGTGGCAGTTAGAGATACAAGACAAACCATCTA
AAACAGATACTGATAGTAGTAACCAAGAAAAAGCATCTACAATGAGCAGCCCAGAAATAGATGAAGAAATTGAGAAAATC
AAAGGATCTAGTGAATAT

Alignment

ORF - retro_nleu_1198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.8 %
• Parental protein coverage: 80.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NSSGEVNEQALKKILSNVKKHVVGWYKFRRHSDQIMTFRERLLHKNLQEHFSNQDLVFLLLTPSIITESC
          NSS.E.NEQAL.KI.SNVKK.V.GWYKFR.HSDQIM.FRERLLHKNLQE.FSNQ.LVFLLLTPSIITESC
Retrocopy NSSSEINEQALQKIFSNVKKNVIGWYKFRHHSDQIMMFRERLLHKNLQEQFSNQELVFLLLTPSIITESC

Parental  STHRLEHSLYKPQKGLFHRVPLVVANLGMSEQLGYKTVSGSCMSTGFHQAVQTHSSKFFEEDGSLKEVHK
          STHRL.H.L.KPQKGLFHRVPLVVANLG.SEQLGYKTVSGSCMSTGF.QAV.THSSKFFEEDGSLKEVHK
Retrocopy STHRLKHAL-KPQKGLFHRVPLVVANLGISEQLGYKTVSGSCMSTGFSQAVKTHSSKFFEEDGSLKEVHK

Parental  INEMYASLQEELKS-ICKKVEDSEQAVDKLVKDVNRLKREIKKRRRAQ-IQAAREKNIQKDPQENIFLCQ
          INE.........K......VED.EQA..KLVKD.NRLK.EI.K......IQAA.EKNI.KDPQ.NIF..Q
Retrocopy INEI*CFITRGIKEYMXXXVEDNEQAINKLVKDINRLKQEIGKKDMTV>IQAA*EKNI*KDPQGNIFPRQ

Parental  ALRTFFPNSEFLHSCVMSLKNRHVSKSSCNYNHHLDVVDNLTLMVEHTDIPEASPASTPQIIKHKALDLD
          AL.TF.P.SEFLHSCVMSLKNRHVSKS.CN.N.HLDVV.NLTLM.EHTDIPEA..AS.PQ.IKHKALDLD
Retrocopy ALWTFYPDSEFLHSCVMSLKNRHVSKS-CNNNLHLDVVANLTLMIEHTDIPEATLASRPQMIKHKALDLD

Parental  D-RWQFKRSRLLDTQDKRSKTDTDSSNQDKVSKMSSPETDEEIEKIKGFGGY
          D.R.................TD..SSNQ.K.S.MSSPE.DEEIEKIKG...Y
Retrocopy D<RFKRSWQLEIQDKPSKTDTD--SSNQEKASTMSSPEIDEEIEKIKGSSEY

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_1198 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013241	1 retrocopy	retro_chof_2580,
Homo sapiens	ENSG00000163322	1 retrocopy	retro_hsap_4024,
Macaca mulatta	ENSMMUG00000015357	2 retrocopies	retro_mmul_1499, retro_mmul_2320,
Nomascus leucogenys	ENSNLEG00000009133	2 retrocopies	retro_nleu_1198 , retro_nleu_661,
Pongo abelii	ENSPPYG00000014898	2 retrocopies	retro_pabe_2208, retro_pabe_3301,
Pan troglodytes	ENSPTRG00000023645	2 retrocopies	retro_ptro_1911, retro_ptro_2728,