RetrogeneDB ID: retro_nleu_2774

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397425.1:559034..560241(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ST6GAL1
• Ensembl ID: ENSNLEG00000006676
• Aliases: None
• Description: None

Sequence

>retro_nleu_2774
CTGGCTCACACCAACCTGCAGAAAAACCTCAGCTGCTGTGTCCTGGCCTTTCTCCTGTTTGCGGTCATCTGTGTGTAGAA
GAAAAAGAAGAAAGGGAATTACTATGATTCCCTTAAATTTCAAACCAAGAAATTCCAGATGTTGAAGAGTCTGGGGAAAG
TGGCCATGAGGTCTTATTCCCAATCTGCATCCTCAAGCAGCACCCAGGACCCCCACAGGGGCAGCCAGGCCCTCAGCAAC
CCCAGAGGCCCAGCCAAGGCTATCCAGAGGCCTCCTTCCAGGTGTGGAACAAGGACAGCTTTTCCAAAAACCTTATCCCC
AGGCTGCAAACCATCTGGAAGAATTATTTAAGCATGAAAAAGTACAAAGTGTCCTACAAGGTGCCAGGGACCACCATTAA
GTTCAGTGCAGAGGCCCCACGCTGCCACCTCCTGGACCACGTGAACGTATCCACAGTAGAGACCACAGATTTTCTCTTCA
GTACCTCTGAGTAGGGGGGTTACCTGCCCAAGGACAGCATTAGGACCAAGGGCAGGTCTTGGGGCAAGTGTGCTGTTTTC
TCATCAGCAGGATCTCTGAAGTCCTCGCAACCGGGCAGAGATCTAGATGATCATGATGCAGTCTTGAGGTTTAATGAGGC
ACCCACAGCCAACTTCCGTCAAGATGTAGCCACAAAAACTACCATTCACCTGCTGAACTCTCAGTTGGTCACCACAAAAA
GGCATTTCCTCAAAGACAGTTTGTACAATGAAGGAATCCTGATTGTATGGGACGCATCTATATATCATTCAGATACTTCA
AAGTGGTACCAGAATCCAGACTATAATTTCTTTAATAACTACATGAGCTATCGTAAGCTGCACCCCAATCAGCCCCTTTA
CATCCTCAAGCCCCAGGTGCCTTGGGATTTGTGGGACATCCTGCAAGAAATCTCCTCAGAAGAGATTCAGTGACACCCCC
ATCATCTGGGATACTTGGTGTCATGATCATGATGATGCTGTGTGACCAGGTAGATATTTATGAGTTCCTCCCATCCAAGC
ATGAGACAGACTGGGGCTGCTACCACCAGCAGTTCTTCAATAGCACCTGCACGATGGGCGCCCACCACCTGCTGCTGTAT
TTGGTGAAGTGCCTCAATGAGGGCACAGATGAGGACACTTACCTACTTGGAAAAGCTACACTGCCTGGCTTCCAGGCCAT
TCACTGC

Alignment

ORF - retro_nleu_2774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MIHTNLKKKFSCCVLVFLLFAVICVWKEKKKGSYYDSFKLQTKEFQVLKSLGKLAMGSDSQSVSSSSTQD
          ..HTNL.K..SCCVL.FLLFAVICV.K.KKKG.YYDS.K.QTK.FQ.LKSLGK.AM.S.SQS.SSSSTQD
Retrocopy LAHTNLQKNLSCCVLAFLLFAVICV*KKKKKGNYYDSLKFQTKKFQMLKSLGKVAMRSYSQSASSSSTQD

Parental  PHRGRQTLGSLRGLAKA-KPEASFQVWNKDSSSKNLIPRLQKIWKNYLSMNKYKVSYKGPGPGIKFSAEA
          PHRG.Q.L...RG.AKA..PEASFQVWNKDS.SKNLIPRLQ.IWKNYLSM.KYKVSYK.PG..IKFSAEA
Retrocopy PHRGSQALSNPRGPAKA<YPEASFQVWNKDSFSKNLIPRLQTIWKNYLSMKKYKVSYKVPGTTIKFSAEA

Parental  LRCHLWDHVNVSMVEATDFPFNTSEWEGYLPKESIRTKAGPWGRCAVVSSAGSLKSSQLGGEIDDHDAVL
          .RCHL.DHVNVS.VE.TDF.F.TSE..GYLPK.SIRTK...WG.CAV.SSAGSLKSSQ.G...DDHDAVL
Retrocopy PRCHLLDHVNVSTVETTDFLFSTSE*GGYLPKDSIRTKGRSWGKCAVFSSAGSLKSSQPGRDLDDHDAVL

Parental  RFNGAPTANFQQDVGTKTTIRLMNSQLVTTEKRFLKDSLYNEGILIVWDPSVYHSDIPKWYQNPDYNFFN
          RFN.APTANF.QDV.TKTTI.L.NSQLVTT...FLKDSLYNEGILIVWD.S.YHSD..KWYQNPDYNFFN
Retrocopy RFNEAPTANFRQDVATKTTIHLLNSQLVTTKRHFLKDSLYNEGILIVWDASIYHSDTSKWYQNPDYNFFN

Parental  NYKSYRKLHPNQPFYILKPQMPWELWDILQEISPEEIQ-PNPPSSGMLGIIIMMTLCDQVDIYEFLPSKR
          NY.SYRKLHPNQP.YILKPQ.PW.LWDILQEIS.EEIQ...PPSSG.LG..IMM.LCDQVDIYEFLPSK.
Retrocopy NYMSYRKLHPNQPLYILKPQVPWDLWDILQEISSEEIQ<VTPPSSGILGVMIMMMLCDQVDIYEFLPSKH

Parental  KTDVCYYYQKFFDSACTMGAYHPLLYEKNLVKHLNQGTDEDIYLLGKATLPGFRTIHC
          .TD...Y.Q.FF.S.CTMGA.H.LLY...LVK.LN.GTDED.YLLGKATLPGF..IHC
Retrocopy ETDWGCYHQQFFNSTCTMGAHHLLLY---LVKCLNEGTDEDTYLLGKATLPGFQAIHC

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_2774 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
Bos taurus	ENSBTAG00000010357	1 retrocopy	retro_btau_1767,
Canis familiaris	ENSCAFG00000013698	1 retrocopy	retro_cfam_2158,
Felis catus	ENSFCAG00000013886	1 retrocopy	retro_fcat_1983,
Macaca mulatta	ENSMMUG00000014905	1 retrocopy	retro_mmul_630,
Nomascus leucogenys	ENSNLEG00000006676	1 retrocopy	retro_nleu_2774 ,
Pongo abelii	ENSPPYG00000014388	1 retrocopy	retro_pabe_3575,