RetrogeneDB ID: retro_nleu_1572

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397299.1:20683698..20685178(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000026903
• Aliases: None
• Description: None

Sequence

>retro_nleu_1572
GGGACACAGAAGGTCACCCCATCTCTGATCTTCGCCATCACAATTGCTACAATCGGCTCTTTCCAATTTGGCTACAACAC
TGGGGTCATCAATGCTCCTGAGACGATTGTAAGGGAATTTATCAACACTTTGAAGGACAAGGCAAATACCCCTCCCTCTG
AGATGTTGCGCTTGTCCCTCTGGTACTTGTCTGTGGCCATATTCTCCATTGGTTGTATGATTGGCTCCTTTTCCGTTGGA
CTCTTTGTCAACAGCTTTGACAGGCGTAAGTCAATGCTTACCGTCAACCTGTTGGCTGTCACTGGTGGCTGCCTTATGGG
ATTGTGTAAAGTAGCTGAGTTGGTTGAAATGCTGATCCTGGCCTACTTGGTTATTGGCTTCTTCTGCAGACTCTGCACAG
TTTTGTGCCCACATACATCGGAGAGATCTCACCTATTGCCCTGCGAGGTGTCTTTGGCACTCTCAACCAGCTGGGCATTG
TTGTTGGAATTCTGGTGGCCCAGATCTTTGATCTGGAATTCATCCTGGGGTCTGAAGACCTATGGCCTGTGCTATTAGGC
TTTCCCATCTCTTCTGCTATGCTACAAAGTGCAGCCCTTCCATTTTGCCCTGAAAGTCCCAGAGTCTTGCTCATTAACAG
AAAAGAAAAGGAGAATGCTAAGGAGATCCTCCAGTGCTTGTGGAGCAGCCAGGATGTATCCCAAGACATCCAGGAGATGA
AAGATGGGAGTGCAAGGATGGCACAAGAAAAGCAAGTCACTGTGCTGGAGCTCTTTAGAGTATCCAGCTACCGACAGCCC
ATCATCATTTCCATCATGTTCCAGCTCTCTCAGCAGCTCTCTGGAATCAATGCTGTGTTCTATTACTCAACAGGAATCTT
TAAGGGTGCAGGTGTTCAAGAGCCCATCTGTGTCACCATCAGTGCGGGTGTGGTTAATAGTATCTTCACTATAGTTTCCC
TATTTCTGGTGGAAAGGGCAGTAAGAAGGACTCTACATATGATAGGCCTTGGAGGGATGGCTTTTTGTTCCATCCTCATG
ACTGTTTGTTTGTTATTGATGGATGAGTGTAATGGGATAAGCTTTGTCTGTATTGGGGCTATCTTGGTCTTTGTGGTCTT
CTTTGAAATTGGGCCAGGCCCCATTCCCTGGTTTATTGTGGCTGAACTCTTCAGCCAGGGCCCTGGCCCAGCTGTGACGA
CAGTGGCCGGCTGCTCCAACTGGACCTCCAACTTCCTAGTCAGATTGCTCTTCCCTTCTGCTACTTACTATTTAGGAGCC
TACATTTTTATTATCTTCACTGACTTCCTCATTACCTTCTTGATCTTTACCTTCTTCAAAGTCCCTGATATGTGTTACAG
GACTTTCGAGGATATCACACAGGCCTTTGAAGGGCAGGCACATGATGCAGATAGATCTGGAAGGACCACGTCATGGAGAT
GAACAGTATCCAGCCTGCTAAGGAGACCACCACCAATGTC

Alignment

ORF - retro_nleu_1572 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.89 %
• Parental protein coverage: 99.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GTQKVTPALIFAITIATIGCFQFGYNIGVINAPEKIIKEFINKTLTDKGNAPPSEVLLTSLWSLSVAIFS
          GTQKVTP.LIFAITIATIG.FQFGYN.GVINAPE.I..EFIN.TL.DK.N.PPSE.L..SLW.LSVAIFS
Retrocopy GTQKVTPSLIFAITIATIGSFQFGYNTGVINAPETIVREFIN-TLKDKANTPPSEMLRLSLWYLSVAIFS

Parental  VGGMIGSFSVGLFVNRFGRRNSMLIVNLLAVTGGCFMGLCKVAKSVEMLILGRLVIGLFCGLCT-GFVPL
          .G.MIGSFSVGLFVN.F.RR.SML.VNLLAVTGGC.MGLCKVA..VEMLIL..LVIG.FC.LCT..FVP.
Retrocopy IGCMIGSFSVGLFVNSFDRRKSMLTVNLLAVTGGCLMGLCKVAELVEMLILAYLVIGFFCRLCT<SFVPT

Parental  YIGELSPTALQGAFGTLNQLGIVVGILVAQIFGLKFILGSEELWPLLLGFTIIPTILQSVALPFCPESPR
          YIGE.SP.AL.G.FGTLNQLGIVVGILVAQIF.L.FILGSE.LWP.LLGF.I....LQS.ALPFCPESPR
Retrocopy YIGEISPIALRGVFGTLNQLGIVVGILVAQIFDLEFILGSEDLWPVLLGFPISSAMLQSAALPFCPESPR

Parental  FLLINRKEEENAKRILQRLWGTQDVSQDIQEMKDESARMSQEKQVTLLELFRVSSYRQPLIISIVLQLSQ
          .LLINRKE.ENAK.ILQ.LW..QDVSQDIQEMKD.SARM.QEKQVT.LELFRVSSYRQP.IISI..QLSQ
Retrocopy VLLINRKEKENAKEILQCLWSSQDVSQDIQEMKDGSARMAQEKQVTVLELFRVSSYRQPIIISIMFQLSQ

Parental  QLSGINAVFYYSRGIFKDAGVQEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCSTLMT
          QLSGINAVFYYS.GIFK.AGVQEPI..TI.AGVVN.IFT.VSLFLVERA.RRTLHMIGLGGMAFCS.LMT
Retrocopy QLSGINAVFYYSTGIFKGAGVQEPICVTISAGVVNSIFTIVSLFLVERAVRRTLHMIGLGGMAFCSILMT

Parental  VSLLLKDNYNGMSFVCIGAILVFVAFFEIGPGPIPWFIVAELFSHGPRPAAMAVASCSNWTSNFLVGLLF
          V.LLL.D..NG.SFVCIGAILVFV.FFEIGPGPIPWFIVAELFS.GP.PA...VA.CSNWTSNFLV.LLF
Retrocopy VCLLLMDECNGISFVCIGAILVFVVFFEIGPGPIPWFIVAELFSQGPGPAVTTVAGCSNWTSNFLVRLLF

Parental  PSAAHYLGAYVFMIFTGFLITFLAFTFFKVPETRGRTFEDITRAFEGQAHSANRSG-KDGVMEMNSIKPA
          PSA..YLGAY.F.IFT.FLITFL.FTFFKVP....RTFEDIT.AFEGQAH.A.RSG.KD.VMEMNSI.PA
Retrocopy PSATYYLGAYIFIIFTDFLITFLIFTFFKVPDMCYRTFEDITQAFEGQAHDADRSG<KDHVMEMNSIQPA

Parental  KETITNV
          KET.TNV
Retrocopy KETTTNV

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_1572 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004556	2 retrocopies	retro_btau_708, retro_btau_709,
Callithrix jacchus	ENSCJAG00000018988	1 retrocopy	retro_cjac_446,
Cavia porcellus	ENSCPOG00000003074	1 retrocopy	retro_cpor_761,
Cavia porcellus	ENSCPOG00000009834	1 retrocopy	retro_cpor_760,
Cavia porcellus	ENSCPOG00000011295	1 retrocopy	retro_cpor_587,
Felis catus	ENSFCAG00000001625	1 retrocopy	retro_fcat_1924,
Homo sapiens	ENSG00000059804	2 retrocopies	retro_hsap_3983, retro_hsap_401,
Gorilla gorilla	ENSGGOG00000016813	1 retrocopy	retro_ggor_398,
Macaca mulatta	ENSMMUG00000000439	2 retrocopies	retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys	ENSNLEG00000026903	2 retrocopies	retro_nleu_1572 , retro_nleu_1904,
Oryctolagus cuniculus	ENSOCUG00000008575	1 retrocopy	retro_ocun_352,
Pongo abelii	ENSPPYG00000004234	1 retrocopy	retro_pabe_3274,
Pongo abelii	ENSPPYG00000004235	1 retrocopy	retro_pabe_315,
Pan troglodytes	ENSPTRG00000004624	1 retrocopy	retro_ptro_2703,
Pan troglodytes	ENSPTRG00000004626	1 retrocopy	retro_ptro_307,