RetrogeneDB ID: retro_nleu_180

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:40537619..40538574(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNMTL1
• Ensembl ID: ENSNLEG00000000570
• Aliases: None
• Description: None

Sequence

>retro_nleu_180
AGAACTTGCAGTGTAATGACACTAGTTAAGTCCAGGCCTTTTCGGGAAAAGCAAGGGAAGATACTGCTGAAAGGTCACAG
GCTCATTGCAGATGATCTCAAGGCTGGAGCTGTGCCGAAAGTTTTCTTCTCTAGCCGTCTATAATACATAAAGAAGCTGC
TCATCAATAAGCTGAAGGGTGTTAGCCTCATTAAGATGAAATTTGAGGACATCAAGGATTGGTCCAACCTAGTAATGCCA
CGAGAATAATGGGGATTTTTGCCAAACCTGACCATGTTAACATGACATATCCAAAGACTCAGCTTTAGCACTCACTGCCT
TTATTATTGATTTGTGACAATCTCTGTGACCCTGGGAACCTGGGGACAATTCTGAGATCTCCAGCTGGGGCAAGCTGCAG
CAAAGTGTTACTCACATTGAAAGGCTGTGTGAATGCCTGGGAGCCCAAAGTGCTACAGGCGGGTATGGGTGCACATTTCC
AGGTGCCCATTATCAATAATCTGAAAATGAAACAGTGCCAAATTACTTGCCCCCTGACACCCAGGTCTGTGTGGCTGACA
GCTGAAGCCTTTATGCTCAGGCTCAGATGTCTAATAAAGCCAGTGACTATGGCTGGGTGTATGATTGGTGATTCCTGAAG
TTTCACAAGTATGAAGAAAAGGAAGGTCTAGAAACTGGAGCCGGTAAAGGTTTGCTGCCTGTTATTGAAGTTCAGAGTTA
TGACTTGGACTGGACAGAGGCACCAACAGCTGTAGTGGTTGGCGGCGGAACCTACGGCATGAGCCTGGAGTCTCTGTAGT
TGGCCGAGAGCCCTGCGGGCAAGAGGCTGCTGATCCCTGTTGCACCTGGAGTGGTCAGCCTCAACTCGGCCATGGCTGCA
CGCATCCTGCTTTTTGAAGGGAAATGACAACTGCGGGTGAGGGCGGAACACTTGAGCAGGGACAGGACTTACCAC

Alignment

ORF - retro_nleu_180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.19 %
• Parental protein coverage: 75.71 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLSSVMTIVKSRPFREKQGKILLEGRRLITDALKAGAVAKTFFFSRLEYLKELPVNKLKGVSLIKVKFED
          R..SVMT.VKSRPFREKQGKILL.G.RLI.D.LKAGAV.K.FF.SRL.Y.K.L..NKLKGVSLIK.KFED
Retrocopy RTCSVMTLVKSRPFREKQGKILLKGHRLIADDLKAGAVPKVFFSSRL*YIKKLLINKLKGVSLIKMKFED

Parental  IKDWSDLVTPQG-IMGIFAKPDHVKMTYPKTQLQHSLPLLLICDNLRDPGNLGTILRSAAGAGCSKVLLT
          IKDWS.LV.P...IMGIFAKPDHV.MTYPKTQL.HSLPLLLICDNL.DPGNLGTILRS.AGA.CSKVLLT
Retrocopy IKDWSNLVMPRE<IMGIFAKPDHVNMTYPKTQL*HSLPLLLICDNLCDPGNLGTILRSPAGASCSKVLLT

Parental  -KGCVDAWEPKVLRAGMGAHFRVPIINNL-EWETVPSYLPPDTRVYVADNCGFYAQAQMSNKASDHGWVC
          .KGCV.AWEPKVL.AGMGAHF.VPIINNL.E.ETVP.YLPPDT.V.VAD....YAQAQMSNKASD.GWV.
Retrocopy LKGCVNAWEPKVLQAGMGAHFQVPIINNL<ENETVPNYLPPDTQVCVADS*SLYAQAQMSNKASDYGWVY

Parental  DQQVLKFHKYEEEEDVETGASQDWLPDVEVQSYCSDWTAAPAAVVIGGETYGVSLESLQLAESTGGKRLL
          D...LKFHKYEE.E..ETGA....LP..EVQSY..DWT.AP.AVV.GG.TYG.SLESL.LAES..GKRLL
Retrocopy DW*FLKFHKYEEKEGLETGAGKGLLPVIEVQSYDLDWTEAPTAVVVGGGTYGMSLESL*LAESPAGKRLL

Parental  IPVVPGVDSLNSAMAASILLFEGKRQLRGRAEQLSRDRSYH
          IPV.PGV.SLNSAMAA.ILLFEGK.QLR.RAE.LSRDR.YH
Retrocopy IPVAPGVVSLNSAMAARILLFEGK*QLRVRAEHLSRDRTYH

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_180 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021701	1 retrocopy	retro_cjac_3130,
Homo sapiens	ENSG00000171861	1 retrocopy	retro_hsap_3704,
Gorilla gorilla	ENSGGOG00000015518	1 retrocopy	retro_ggor_2505,
Macaca mulatta	ENSMMUG00000011423	1 retrocopy	retro_mmul_1709,
Nomascus leucogenys	ENSNLEG00000000570	1 retrocopy	retro_nleu_180 ,
Pongo abelii	ENSPPYG00000007762	1 retrocopy	retro_pabe_3149,