RetrogeneDB ID: retro_nleu_826

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397274.1:17703215..17704732(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISYNA1
• Ensembl ID: ENSNLEG00000006026
• Aliases: None
• Description: None

Sequence

>retro_nleu_826
CGGCAGGTGCCCAGGCTAGGGGTCATGCTTGTCGCCTGGGGTGGGAACAACGGTTCCACGCACCGGTTCCGCGGTGCTGG
CCAACCTACTGCGTCTGTCCTGGCCCAAGCGCAGGGGTCGTAAGGGGGCCAACTACTACGGTTCGCTGTCTCAGGCGGGC
ACCGTGAGCCCGGGCCTGGACGCCAAGGGCTAGGAGGTGTTCGTGCCCTTCCGCGGCTGCTGCCCATGGTGGCGCCCAAC
GACCTCGTGTTCGATGGCTGAGACATCTTGTCGCCGAACCTGGCCGAGGCGATGCGGCTCGCAAAGGTGCTGGATTGGGG
GCTGCAGGAGCAACTGTGGCCACACATGGAGGCCCTGCAGCCCCGGCCTTTGGTATACATCCCAGAGTTCATCGCGGCCA
ACCAGAACACGCGCGCGGACAGCCTCATCCCGGGCACGCGCGCGCAGCAGCTGGAGCAGATCCGCCGGGACATCCGAGAC
TTCCGGTCTAGCGCAGGGCTGGACAAAGTCATAGCGCTGTGAACGGCGCACAGGGAGCGCTTCTTTGAGGTGGTCCCACG
TCTCAACAACACGGCCGAGAAACTGCTGCGCACGATCGAGCTTGGCCTGAAGGTGTCGCCCTCCACGCTCTTCGCCGTGG
CCAGCATCCTGGAGGGCTGTGCCTTCCTCAGTGGGTCCCCACAGGACACCCTGGTGCCCGGAGTCCTTGAGCCCGCGTGG
CAGCGCCAGGTTTACGTGGGCGGAGATGACTTCAAGTCAGGCCAGACCAAAGTCAAGTCCGTGCTCGTAGACTTCCTCAT
TGGCTACGGCCTCAAGACCAAGTCGATTGTGAATTATAACTACCTGGGGAACAGCGACCGGCAGAACCTGTTGGCGCCAT
CGCGGTTCCCTCTGAGGAGGTGTCCAAGAGCAACGTGGTGGACGACATGGTGCAAAGACACCCAGTGCTCTACGCGCCCT
GCGAGGAGCGTGACCGCTGCGTGGTCATCAAGTACATGCCGTACGCAGGCGACCCCATGCATGTGCTGGATGAGTCTACC
TTGGAGCTGATGCTGGGCGTAAGCAACACGCTGGTACTGCACAACACGTGCGAGGACTCGCTGCTGGCCGCCCCCATCAT
CCTGGACCTGGCGCTGCTGACCGAGCTGTGCCACTGCGTGAGCTTCTGCACCAATGACAACACCGAGCCACAGACCTTCC
ACCCCGTGCTGTCCCTGCTTAGCATCCTCTTCAAGGAGCCGCTGGTGCCGCCGGGCAGCCCGGTGGTCAATGTGGTTTTC
CGCCAGCTCAGCTGCATCGAGAACATCGTCAGGGCCTGTGTGGGGCTTCCGCCACAGAACCACGTGGTCCTGGAGCACAA
GATGGAGCTCCCAGTGCCTGGCCTCAAGCGAGTCGGACCCGTGGCTGCTGCCTGCCCTGTGTCGAACAAGAAAGGACCGG
TACCTGCTGCCACCAATGGCTGTACCGGTGATACCAATGGACACCCACAAGCGGAGGAACCCCAGATGCACACCACC

Alignment

ORF - retro_nleu_826 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.75 %
• Parental protein coverage: 90.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RQVPRLGVMLVGWGGNNGST-LTAAVLANRLRLSWPTRSGRKEANYYGSLTQAGTVSLGLDAEGQEVFVP
          RQVPRLGVMLV.WGGNNGST....AVLAN.LRLSWP.R.GRK.ANYYGSL.QAGTVS.GLDA.G.EVFVP
Retrocopy RQVPRLGVMLVAWGGNNGST>TGSAVLANLLRLSWPKRRGRKGANYYGSLSQAGTVSPGLDAKG*EVFVP

Parental  FSA-LLPMVAPNDLVFDGWDISSLNLAEAMRRAKVLDWGLQEQLWPHMEALRPRPSVYIPEFIAANQSAR
          F...LLPMVAPNDLVFDG.DI.S.NLAEAMR.AKVLDWGLQEQLWPHMEAL.PRP.VYIPEFIAANQ..R
Retrocopy FRG<LLPMVAPNDLVFDG*DILSPNLAEAMRLAKVLDWGLQEQLWPHMEALQPRPLVYIPEFIAANQNTR

Parental  ADNLIPGSRAQQLEQIRRDIRDFRSSAGLDKVIVLWTANTERFCEVIPGLNDTAENLLRTIELGLEVSPS
          AD.LIPG.RAQQLEQIRRDIRDFRSSAGLDKVI.L.TA..ERF.EV.P.LN.TAE.LLRTIELGL.VSPS
Retrocopy ADSLIPGTRAQQLEQIRRDIRDFRSSAGLDKVIAL*TAHRERFFEVVPRLNNTAEKLLRTIELGLKVSPS

Parental  TLFAVASILEGCAFLNGSPQNTLVPGALELAWQRRVFVGGDDFKSGQTKVKSVLVDFLIGSGLKTMSIVS
          TLFAVASILEGCAFL.GSPQ.TLVPG.LE.AWQR.V.VGGDDFKSGQTKVKSVLVDFLIG.GLKT.SIV.
Retrocopy TLFAVASILEGCAFLSGSPQDTLVPGVLEPAWQRQVYVGGDDFKSGQTKVKSVLVDFLIGYGLKTKSIVN

Parental  YNHLGNNDGENLSAPLQF-RSKEVSKSNVVDDMVQSNPVLYTPGEEPDHCVVIKYVPYVGDSKRALDEYT
          YN.LGN.D..NL.AP..F..S.EVSKSNVVDDMVQ..PVLY.P.EE.D.CVVIKY.PY.GD....LDE.T
Retrocopy YNYLGNSDRQNLLAPSRF<PSEEVSKSNVVDDMVQRHPVLYAPCEERDRCVVIKYMPYAGDPMHVLDEST

Parental  SELMLGGTNTLVLHNTCEDSLLAAPIMLDLALLTELCQRVSFCTDMDPEPQTFHPVLSLLSFLFKAPLVP
          .ELMLG..NTLVLHNTCEDSLLAAPI.LDLALLTELC..VSFCT....EPQTFHPVLSLLS.LFK.PLVP
Retrocopy LELMLGVSNTLVLHNTCEDSLLAAPIILDLALLTELCHCVSFCTNDNTEPQTFHPVLSLLSILFKEPLVP

Parental  PGSPVVNALFRQRSCIENILRACVGLPPQNHMLLEHKMERPGPGLKRVGPVAATYPVLNKKGPLPATTNG
          PGSPVVN..FRQ.SCIENI.RACVGLPPQNH..LEHKME.P.PGLKRVGPVAA..PV.NKKGP.PA.TNG
Retrocopy PGSPVVNVVFRQLSCIENIVRACVGLPPQNHVVLEHKMELPVPGLKRVGPVAAACPVSNKKGPVPAATNG

Parental  CTGDANGHLQVEEPPMPTT
          CTGD.NGH.Q.EEP.M.TT
Retrocopy CTGDTNGHPQAEEPQMHTT

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_826 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 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014230	6 retrocopies	retro_cjac_2768, retro_cjac_2803, retro_cjac_2809, retro_cjac_2831, retro_cjac_3817, retro_cjac_435,
Homo sapiens	ENSG00000105655	1 retrocopy	retro_hsap_2918,
Gorilla gorilla	ENSGGOG00000016939	1 retrocopy	retro_ggor_2019,
Nomascus leucogenys	ENSNLEG00000006026	1 retrocopy	retro_nleu_826 ,