RetrogeneDB ID: retro_nleu_232

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:59757445..59758763(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTBD10
• Ensembl ID: ENSNLEG00000017691
• Aliases: None
• Description: None

Sequence

>retro_nleu_232
AGTACTTCCTCGCATATTGCAAAAGGAGTCGACCACACCAAAGTGAGCCTACATGATGCTAGCGGGGGTTGTAAGAGGTC
AAGAGATAGACAAACGTCAAGTGACAGATCACGAGATTCATCTCATGAAAGAACAGTCTCAACTCACTCCTTGTATTAGA
AATGTGACTTCTCCAACATGACAGCACCATGTTGAACAAGAAAAAGATCGCAGTTCCTCTCGTCCAAGCAGTCTGCGTCC
TCAAAAAGCATCCCCAAATGGTTCCATTAGCAGTGCTGGGAACAGCAGCAGAAACAGTAGTCAGTCAAGTTTAGGTGGTA
GCTGTAAGACATCTAGGGAGATGGTGTTTGTATATGAAAATGCAAAAGAAGGAGCTCAGAATATAAGAACGTCAGAACGA
GTGACACTAATAGTGGATAACACTAGATTTCTTGTAGACCCATCCATTTTTACTGCACAGCCAAATACAATGTTGGGCAG
GATGTTTGGTTCTGGCCGAGAACATAACTTTACACGACCCAATAAGAAAGAAGAGTATGAGGTGGCAGAGGGGATTGGTT
CCACTGTGTTTCAGGCTATTCTGGATTACTATAAAACAGGAATAATCCATTGTCCTGATGGCATATCTATTCCTGAACTG
AGAGAAGCATGTGACTATCTTTGTATCTCTTTTGAATATAGTACTGGTAAATGTAAAGATCTCAGTGCCCTAATGCATGA
GTTATCAAATGATGGTGCTCATAGACAATTTGAATTTTATCTGGAAGAAATGATCCTCCCTCTCATGGCAGCTAGTGCCC
AGAGGGGGGAATGGGAATGTCATATAGTGGTGCTTACAGATGATGATGTGGTTGATTGGGATGAAGAATATCCACCACAG
ATTGGAGAATAATATTCACAAATTATTTATAGCACAAAATTATATAGATTTTTCAAGTACATTGAAAACAGAGATGTGGC
CAAGTCAGTTTTGAAGAACAGGGGTCTTAAGATTAGATTGGGAATAGAAGGTTATCCTACCTACAAAGAAAAAGTAAAGA
AAAGGCCTAGAGGCCGCCCAGAAGTGATCTACAACTATGTCCAAAGACCCTTTATTCGAATGTCCTGGGAGAAGGAAGAA
GGAAAGAGTCAGCATGTAGACTTTCAGTGTGTAAAGAGTAAATCTACCACCAACCTTGCAGCAGCTATGGCAGACATTCC
CCAGGACCAGCTGGTAGTCATGCACCCAACTCCACGAGTGGATGAGCTGGATATTCTCCCCATCCATCCCCCTTCTGGCA
ATGGTGGCCTCGATCCTGATGCACAGAATCCAATGCTG

Alignment

ORF - retro_nleu_232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.49 %
• Parental protein coverage: 93.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STSSRIAKGGVDHTKMSLHGASGGHERSRDRRRSSDRSRDSSHE-RTESQLTPCIRNVTSPTRQHHVERE
          STSS.IAKG.VDHTK.SLH.ASGG..RSRD.R..S......S......SQLTPCIRNVTSPT.QHHVE.E
Retrocopy STSSHIAKG-VDHTKVSLHDASGGCKRSRD-RQTSSDRSRDSSH>KEQSQLTPCIRNVTSPT*QHHVEQE

Parental  KDHSSSRPSSPRPQKASPNGSISSAGNSSRNSSQSSSDGSCKTSGEMVFVYENAKEGARNIRTSERVTLI
          KD.SSSRPSS.RPQKASPNGSISSAGNSSRNSSQSS..GSCKTS.EMVFVYENAKEGA.NIRTSERVTLI
Retrocopy KDRSSSRPSSLRPQKASPNGSISSAGNSSRNSSQSSLGGSCKTSREMVFVYENAKEGAQNIRTSERVTLI

Parental  VDNTRFVVDPSIFTAQPNTMLGRMFGSGREHNFTRPNEKGEYEVAEGIGSTVFRAILDYYKTGIIRCPDG
          VDNTRF.VDPSIFTAQPNTMLGRMFGSGREHNFTRPN.K.EYEVAEGIGSTVF.AILDYYKTGII.CPDG
Retrocopy VDNTRFLVDPSIFTAQPNTMLGRMFGSGREHNFTRPNKKEEYEVAEGIGSTVFQAILDYYKTGIIHCPDG

Parental  ISIPELREACDYLCISFEYSTIKCRDLSALMHELSNDGARRQFEFYLEEMILPLMVASAQSGERECHIVV
          ISIPELREACDYLCISFEYST.KC.DLSALMHELSNDGA.RQFEFYLEEMILPLM.ASAQ.GE.ECHIVV
Retrocopy ISIPELREACDYLCISFEYSTGKCKDLSALMHELSNDGAHRQFEFYLEEMILPLMAASAQRGEWECHIVV

Parental  LTDDDVVDWDEEYPPQMGEEYSQIIYSTKLYRFFKYIENRDVAKSVLKERGLKKIRLGIEGYPTYKEKVK
          LTDDDVVDWDEEYPPQ.GE.YSQIIYSTKLYRFFKYIENRDVAKSVLK.RGL.KIRLGIEGYPTYKEKVK
Retrocopy LTDDDVVDWDEEYPPQIGE*YSQIIYSTKLYRFFKYIENRDVAKSVLKNRGL-KIRLGIEGYPTYKEKVK

Parental  KRPGGRPEVIYNYVQRPFIRMSWEKEEGKSRHVDFQCVKSKSITNLAAAAADIPQDQLVVMHPTPQVDEL
          KRP.GRPEVIYNYVQRPFIRMSWEKEEGKS.HVDFQCVKSKS.TNLAAA.ADIPQDQLVVMHPTP.VDEL
Retrocopy KRPRGRPEVIYNYVQRPFIRMSWEKEEGKSQHVDFQCVKSKSTTNLAAAMADIPQDQLVVMHPTPRVDEL

Parental  DILPIHPPSGNSDLDPDAQNPML
          DILPIHPPSGN..LDPDAQNPML
Retrocopy DILPIHPPSGNGGLDPDAQNPML

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_232 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024984	1 retrocopy	retro_cpor_137,
Monodelphis domestica	ENSMODG00000008728	1 retrocopy	retro_mdom_1020,
Mus musculus	ENSMUSG00000038187	1 retrocopy	retro_mmus_3560,
Nomascus leucogenys	ENSNLEG00000017691	1 retrocopy	retro_nleu_232 ,
Otolemur garnettii	ENSOGAG00000000739	1 retrocopy	retro_ogar_3201,
Pan troglodytes	ENSPTRG00000003377	1 retrocopy	retro_ptro_753,
Rattus norvegicus	ENSRNOG00000014341	2 retrocopies	retro_rnor_2220, retro_rnor_2872,
Sorex araneus	ENSSARG00000000266	1 retrocopy	retro_sara_405,
Sus scrofa	ENSSSCG00000013395	2 retrocopies	retro_sscr_639, retro_sscr_640,
Tarsius syrichta	ENSTSYG00000000445	2 retrocopies	retro_tsyr_196, retro_tsyr_367,
Tursiops truncatus	ENSTTRG00000013943	1 retrocopy	retro_ttru_897,