RetrogeneDB ID: retro_nleu_1073

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397280.1:25160710..25163370(+)
• Located in intron of: ENSNLEG00000016874

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM35A
• Ensembl ID: ENSNLEG00000011652
• Aliases: None
• Description: family with sequence similarity 35, member A [Source:HGNC Symbol;Acc:28773]

Sequence

>retro_nleu_1073
CCTGTTGCTCCACTAAAAATGACAGTATCACAAGACACAGCTTCTTTAATGTCCATTGCTGACCCCTGGAAAAAAATTCA
TTTTTATACAGTCAACATTCTTCATATCTGAAGGATGAAAAACAGCACAAAAATCTTGAAAACTATGAAGTCCCAGAATC
TATTGGTTCTCCAGATCTCAGTGGTCATTTCTTAGCAAACTGTATGAATAGACATGTTCATGTGAAAGATAACTTTGTAC
ATTCTGTTTCTGAAACACAGAATATAGAATCCCAGAAGATTCACTCATCTAAACTGAGTGATGTAACTAGCTCTAATATG
CAAATATGTGGATTTAAAACCACAGTTCCACATTTAACTGAAAAGTATCAAAAGCTTCTCAGTGAAAATAAAATTATAGA
TGAACAGCCTAAACATCAGTCAGATATATGTGGTCAGAACTTTAACACAAATTTGTTTCAGTTAGGCCATAAATGTGCAG
CTATGTTGGATTTGGTTTGTAGTACTAAACAAATTAATATAGGGCCTGAAGTGGTACAAAGAGAGTGTGTGCCAACAGAA
TATCATGAAATACAAAACCGGTGTTTGGGATTATTTTCCTTGAACACAGTAGATAAGCCAAGGTCTGAAGCAGCAGTTAG
GAAGGTCTCCGACCTTAAAATATCAACTGATACCGAATTTCTCAGTATAATTACCTCCAGCCAGGTTGCTTTTTTAGCTC
AAAAGAAAGATAAAGGGAGGAGTCCTATAAATAAAGGGAATGTAAACATGGAGACTGAACCAAAGGCAAGTTACAGGGAG
ATAAGAATACCTGAAGAGAATTCGATTCAACTTGATGATTTTACAGAAGCATACGAAAGTGGACAAAACCAAGCATATTC
CCTTGAACATTTTAGTCCTGTTTGTCCTAAAACAGAAAACAGCCACATTCACATAAACTCTGATAAAGGTCTTGAAGAAA
ATACAGGATCTCAAGAACTTTTCAGTTCTGAAGACGAACCGCCACCAAATGAGATACGTATTGAGTTGTGTAGCTCAGGA
ATACTGTGTTCAGAACTAAATACCTTCCACAAAAGCGCTACTAAAAGAAGCTGCACCTCTGAAGATAAAGTAGACCAGTC
TGAAGCTCTATCTAGAGTCCTTCAAGGAGCTAAGAAAATGAAGTTGATTTCTAATGCAGGAGATTCTGCTGTAGAAATGG
ATCAGAGGAATGTGTCTGAATTTAAGGGTATTAAAAAAGTCATTAATAAAAAACTGTGATTCTAAAAGCCAGAAGTATAA
TTGTTTAGTCATGGTGCTATCTCCATGCCATGTGAAGGAAATAAACATAAAATTCAGACCAAATTCTGGCTTTAAAGTGC
CTTTAGCAACAGTTACAGTAATTGATCAATCAGAAACTAAGAAGGTTTTTCTGTGGAGGACTGCAGCATTTTGGCCATTT
ACAGTGTTTCTTGGAGATATAATTTTACTCGCAGATGTTGTTATTCATGAGGACCAATGGGTTGGCGAGACAGTACTACA
ATCAACATTTAGCAGTCAGTTATTAAATCTTGGGAGTTATTCATCTATTCATCCTGAAGAATATTCCAGTGTAGTTAGTG
ATGTTGTACTTCAAGACTTACTGGCACATGTGTCCTCAAAACATTCCTACCTCAGAGATCTTGCTCCGAGGCAGCCTCAG
AGGGTGAACAGTATAGACTTTGTAGAACTGGAGCACCTTCAGCCTGACGTATTAGTCCACACAATACTAAGAGTTGTTGA
TTTCACTATACTGACAGACGCAGTATACAGTTATAGAGGACAGAAGCAGAAAAAAGTTATGTTAACAGTGGAACAGGCCC
AAGATCAACATTATGTGCTTGTATTATGGGGTCCTGGAGCAGCCTGGTACCCTCAACTTCAAAGGAAAAAAGGTTATATT
TGGGAATTCAAATATATTTTTGTTCAGCGCAATTACATACTAGAAAACCTAAAATTGCATACAATGCCTTGGTCATCCTG
TGAGTGCTTGTTTGATGATGATATAAGGGCAGTTACATTTAAAGCAAAATTTCAAAAAAGTGCACCCTCCTTTGGGAAGA
TATCAGACTTAGCAACCCACCTAGAGGATAAATGTTCAGGAGTGGTTCTAATTAAAGCCCAGATTTCAGAGCTGTCATTT
CCTACTACGGCAGCTCAGAAGATAGCTCTAAATGCTCACAGTTCTCCGAAGAGTATTTTTTCTTCTCTTCCCAACATCGT
ATATACTGGCTGCGCAAAATGTGGATTGGAACTAGAAACAGTTGAGAACAGGATCTACAAACAATGTTTTAGCTGCTTGC
CATTTACTATGAAGAAAATATACTATAGGCCATCCTTAATGACTGTAGTTGATGGAAGACATGATGTTTGCATCATGTAG
AATCAAAGCTGATAGAGAAGATTCTTCTCAACATTTCTGCAGGCTGCCTCAACGGAGTGATAGTTCCTTCCTCAGGGATC
ACCTATGGGATGGTCGTGGCAGACCTGTTCCACTCCTTGTTGGCAGTCAGCGCAGAACCTTGTGTATTAAAGATTCAGAG
CTTTTTTGTGTTAGATGAAAACAGCTATCCATTACAACAAGATTTCTCCCTCCTGGATTTTTATCCTAACATTCTAAAGC
ATGGAGCCGATGCCCTTCTC

Alignment

ORF - retro_nleu_1073 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.6 %
• Parental protein coverage: 98.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PVAPLKMTISQGTASLMSVADPWKKIQL-LYSQHSLYLKDEKQHKNLENYEVPESIGSPDVSGHFLANCM
          PVAPLKMT.SQ.TASLMS.ADPWKKI...LYSQHS.YLKDEKQHKNLENYEVPESIGSPD.SGHFLANCM
Retrocopy PVAPLKMTVSQDTASLMSIADPWKKIHF<LYSQHSSYLKDEKQHKNLENYEVPESIGSPDLSGHFLANCM

Parental  NRHVHVKDDFVRSVSETQNIESQKIHSSRLSDITSSNMQICGFKSTVPHLAKEEKDQKLLSENKIIDEQP
          NRHVHVKD.FV.SVSETQNIESQKIHSS.LSD.TSSNMQICGFK.TVPHL...EK.QKLLSENKIIDEQP
Retrocopy NRHVHVKDNFVHSVSETQNIESQKIHSSKLSDVTSSNMQICGFKTTVPHLT--EKYQKLLSENKIIDEQP

Parental  KHQADICGQNFNTDLFQLGHKCAAILDLVCSTEQINIGPEVVQRECVPTEYHEIQNQCLGLFSSNAVDNS
          KHQ.DICGQNFNT.LFQLGHKCAA.LDLVCST.QINIGPEVVQRECVPTEYHEIQN.CLGLFS.N.VD..
Retrocopy KHQSDICGQNFNTNLFQLGHKCAAMLDLVCSTKQINIGPEVVQRECVPTEYHEIQNRCLGLFSLNTVDKP

Parental  RSEAAVRKVSDLKISTDTEFLSIITSSQVAFLAQKKDKGRSPINKGNVNMEAEPKASYGEIRIPDENSIQ
          RSEAAVRKVSDLKISTDTEFLSIITSSQVAFLAQKKDKGRSPINKGNVNME.EPKASY.EIRIP.ENSIQ
Retrocopy RSEAAVRKVSDLKISTDTEFLSIITSSQVAFLAQKKDKGRSPINKGNVNMETEPKASYREIRIPEENSIQ

Parental  LDGFTEAYESGQNQAYSLELFSPVCPKTENSCIHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSG
          LD.FTEAYESGQNQAYSLE.FSPVCPKTENS.IHINSDKGLEE.TGSQELFSSEDE.PPNEIRIELCSSG
Retrocopy LDDFTEAYESGQNQAYSLEHFSPVCPKTENSHIHINSDKGLEENTGSQELFSSEDEPPPNEIRIELCSSG

Parental  ILCSQLNTFHKSAIKRSCTSEDKVGQSEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKG-IKKTSL
          ILCS.LNTFHKSA.KRSCTSEDKV.QSEALSRVLQ.AKKMKLISN.GDSAVEMD.RNVSEFKG..KK.SL
Retrocopy ILCSELNTFHKSATKRSCTSEDKVDQSEALSRVLQGAKKMKLISNAGDSAVEMDQRNVSEFKG>LKK-SL

Parental  IKNCDSKSQKYNCLVMVLSPCHVKEINIKCGRNSGSKVPLATVTVIDESETKKKVFLWRTAAFWAFTVFL
          IKNCDSKSQKYNCLVMVLSPCHVKEINIK...NSG.KVPLATVTVID.SETKK.VFLWRTAAFW.FTVFL
Retrocopy IKNCDSKSQKYNCLVMVLSPCHVKEINIKFRPNSGFKVPLATVTVIDQSETKK-VFLWRTAAFWPFTVFL

Parental  GDIILLTDVVIHEDQWVGETVLQSTFSTQLLNLGSYSSIQPEECSSVVSDVVLQDLLAYVSSKHSYLRDL
          GDIILL.DVVIHEDQWVGETVLQSTFS.QLLNLGSYSSI.PEE.SSVVSDVVLQDLLA.VSSKHSYLRDL
Retrocopy GDIILLADVVIHEDQWVGETVLQSTFSSQLLNLGSYSSIHPEEYSSVVSDVVLQDLLAHVSSKHSYLRDL

Parental  PPRQPQRVNSIDFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWG
          .PRQPQRVNSIDFVELEHLQPDVLVH..LRVVDFTILT.AVYSYRGQKQKKVMLTVEQAQDQHYVLVLWG
Retrocopy APRQPQRVNSIDFVELEHLQPDVLVHTILRVVDFTILTDAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWG

Parental  PGAAWYPQLQRKKGYIWEFKYLFVQRSYTLENLELHTTPWSSCECLFDDDIRAITFKAKFQKSAPSFVKI
          PGAAWYPQLQRKKGYIWEFKY.FVQR.Y.LENL.LHT.PWSSCECLFDDDIRA.TFKAKFQKSAPSF.KI
Retrocopy PGAAWYPQLQRKKGYIWEFKYIFVQRNYILENLKLHTMPWSSCECLFDDDIRAVTFKAKFQKSAPSFGKI

Parental  SDLATHLEDKCSGVVLIKAQISELAFPITAAQKIALNAHSSLKSIFSSLPNIVYTGCAKCGLELETDENR
          SDLATHLEDKCSGVVLIKAQISEL.FP.TAAQKIALNAHSS.KSIFSSLPNIVYTGCAKCGLELET.ENR
Retrocopy SDLATHLEDKCSGVVLIKAQISELSFPTTAAQKIALNAHSSPKSIFSSLPNIVYTGCAKCGLELETVENR

Parental  IYKQCFSCLPFTRKKIYYRPVLMTVIDGRHDVCI-RVESKLIEKILLNISADCLNRVIVPSSEITYGMVV
          IYKQCFSCLPFT.KKIYYRP.LMTV.DGRHDVCI..VESKLIEKILLNISA.CLN.VIVPSS.ITYGMVV
Retrocopy IYKQCFSCLPFTMKKIYYRPSLMTVVDGRHDVCI<HVESKLIEKILLNISAGCLNGVIVPSSGITYGMVV

Parental  ADLFHSLLAVSAEPCVLKIQSLFVLDENSYPLQQDFFLLDFYPDIVKHGADGCL
          ADLFHSLLAVSAEPCVLKIQS.FVLDENSYPLQQDF.LLDFYP.I.KHGAD..L
Retrocopy ADLFHSLLAVSAEPCVLKIQSFFVLDENSYPLQQDFSLLDFYPNILKHGADALL

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_1073 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000017	1 retrocopy	retro_dnov_2237,
Homo sapiens	ENSG00000122376	1 retrocopy	retro_hsap_1370,
Nomascus leucogenys	ENSNLEG00000011652	3 retrocopies	retro_nleu_1073 , retro_nleu_2157, retro_nleu_840,
Pongo abelii	ENSPPYG00000002828	1 retrocopy	retro_pabe_1137,
Pan troglodytes	ENSPTRG00000002465	1 retrocopy	retro_ptro_941,