RetrogeneDB ID: retro_nleu_2344

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397347.1:2395817..2397130(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5DC1
• Ensembl ID: ENSNLEG00000013080
• Aliases: None
• Description: None

Sequence

>retro_nleu_2344
GGATTCTACCTGGACCACACCCTATGTCACTACAACCTGCCCGAGAGCGCCCCACTCATTTATAATAGCTTTGCCCAGTT
CTTAGTTAAGGAGAAAGGGTATAATAAGGAATTGCTCAATGTGACCCCAGAGGATTGGAATTTCTGTTGCAAGGGTTTGG
CATTGGATCTAGAAGATAGGAACTTCCTTAAACTTGCTGATAATGGCACTGTTCTCAGGGCAAGCCATGGCACCAAGATG
ATGACTCCAGAGGTGCTGGCAGAGACATATGGCAAGAAAGTGTGGAAACACTTCTTGTCGGGCACTGGAATGGCTTGCCG
CTCATGAAAGTATTATTTTTACAACTACTTTGACCTGCCAGGAGCTCTTCTATGTGCCAGGGTGATGGACTATTTAACAA
CAAACAATGGTCAAAAAACATTTGATTTTTGGAAGGATATAGTTGCTGCTATACAACACAATTATAAAATGTCAGCTTTT
AAGGAAAACTGTGGAATGTGTTTTCCAGAAGTAAAAAGAGATCCAGGCAGATATTTACACAGTTGTCCTGAATCTGTGAA
AAAATGGCTTCGACAGCTAAAGAATGCTGGGAAAATTCTTCTGTTAATTACCAGTTCTCACAATGATTACTGTAGACTTC
TCTGCAAATATATCCTTGAGAATGATTTTGCAGACCTTTTTGACATTGTGATTACAAATACATTGAAGCCTGGTTTCTTC
TCCCACTTACCAAGTCAGAGACCTTTCTGGATGCAGAGAATGACGAGGAGCAGGAGGCGCTGCCATCTCTGGATAAACCT
GGCTGGTGCTCCCAAGGGAACGCTGTCCACCTCTATGAACTTCTGAAGAAAATCACTGGCAAACCTGAACCCAAGGTTGT
TTATTACAGCATGCATTCAGATATTTTCCTGGCTCGTCACTATAGTAATTGGGAGACAGTTCTTATCCTGGAAGAACTCA
GAGGGATGAAGGTGCAAGGAGTCAGAGGCCTGAGAAGTCAGAGCCTCTAGAGAAAAAGGAAAATATGAGGGACCAAAGGC
AAAGCCTCTAAATACTTCATCTAAAAAATGGGGCTCCTTTTTTTTACTGATTCAGTTTTGGGACTGGAAAATACAGAAGA
CTCCTTTGTTTGTACATAGTCTTGTAAGAGAATCAGTACTTACAGCACTATTGCAATTCCAAGTATTGAAATAATCGCAG
AATTACCTCTGGACTACAAATTTGCAAGATTCTCTTCAAGCAATTCAAAAACAGCTGGCTACTATCCAAACCCTCCATTG
GTCTTATCAAATGATGGGACACTGATAACTAAA

Alignment

ORF - retro_nleu_2344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.13 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GFDLDHTLCRYNLPESARLIYNSFAQFLVKEKGYDKELLNVTPEDFFFCCKGLALDLEDGNFLKLANNGT
          GF.LDHTLC.YNLPESA.LIYNSFAQFLVKEKGY.KELLNVTPED..FCCKGLALDLED.NFLKLA.NGT
Retrocopy GFYLDHTLCHYNLPESAPLIYNSFAQFLVKEKGYNKELLNVTPEDWNFCCKGLALDLEDRNFLKLADNGT

Parental  VLRASHGTKMMTPEVLAEAYGKKEWKHFLSDTGMACRSGKYYFYDNYFDLPGALLCARVVDYLTKQNNGQ
          VLRASHGTKMMTPEVLAE.YGKK.WKHFLS.TGMACRS.KYYFY.NYFDLPGALLCARV.DYLT..NNGQ
Retrocopy VLRASHGTKMMTPEVLAETYGKKVWKHFLSGTGMACRS*KYYFY-NYFDLPGALLCARVMDYLTT-NNGQ

Parental  KTFDFWKDIVAAIQHNYKMSAFKENCGIYFPEIKRDPGRYLHSCPESVKKWLRQLKNAGKILLLITSSHS
          KTFDFWKDIVAAIQHNYKMSAFKENCG..FPE.KRDPGRYLHSCPESVKKWLRQLKNAGKILLLITSSH.
Retrocopy KTFDFWKDIVAAIQHNYKMSAFKENCGMCFPEVKRDPGRYLHSCPESVKKWLRQLKNAGKILLLITSSHN

Parental  DYCRLLCEYILGNDFTDLFDIVITNALKPGFFSHLPSQRPF-RTLENDEEQEVLPSLDKPGWYSQGNAVH
          DYCRLLC.YIL.NDF.DLFDIVITN.LKPGFFSHLPSQRPF....ENDEEQE.LPSLDKPGW.SQGNAVH
Retrocopy DYCRLLCKYILENDFADLFDIVITNTLKPGFFSHLPSQRPF<LDAENDEEQEALPSLDKPGWCSQGNAVH

Parental  LYELLKKMTGKPEPKVVYFGDSMHSDIFPARHYSNWETVLILEELRG-DEGARSQRPEGSEPLEKK-GKY
          LYELLKK.TGKPEPKVVY...SMHSDIF.ARHYSNWETVLILEELRG.DEGARSQRPE.SEPLEKK.GKY
Retrocopy LYELLKKITGKPEPKVVYY--SMHSDIFLARHYSNWETVLILEELRG<DEGARSQRPEKSEPLEKK<GKY

Parental  E-GPKAKPLNTSSKKWG-SFFIDSVLGLENTEDSLVYTWSCKRISTYSTIAIPSIEAIAELPLDYKFTRF
          E.G.K.K.......K.G.....DSVLGLENTEDS.V.T.SCKRISTYSTIAIPSIE.IAELPLDYKF.RF
Retrocopy E<GTKGKASKYFI*KMGLXXXTDSVLGLENTEDSFVCT*SCKRISTYSTIAIPSIEIIAELPLDYKFARF

Parental  SSSNSKTAGYYPNPPLVLSSDETLISK
          SSSNSKTAGYYPNPPLVLS.D.TLI.K
Retrocopy SSSNSKTAGYYPNPPLVLSNDGTLITK

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_2344 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000178425	1 retrocopy	retro_hsap_4759,
Myotis lucifugus	ENSMLUG00000008313	1 retrocopy	retro_mluc_306,
Nomascus leucogenys	ENSNLEG00000013080	1 retrocopy	retro_nleu_2344 ,
Pongo abelii	ENSPPYG00000016943	1 retrocopy	retro_pabe_3703,
Pan troglodytes	ENSPTRG00000018523	1 retrocopy	retro_ptro_3170,