RetrogeneDB ID: retro_nleu_959

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397277.1:5136144..5137407(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RUFY3
• Ensembl ID: ENSNLEG00000007716
• Aliases: None
• Description: None

Sequence

>retro_nleu_959
TTTCTTGGACAAAATATATCCTTCTGGGGGGCTCTAGAACTGGTAGAAAAGCTTGTTCCAGGAGCCGCAGAGATAACAGC
AAGTGTTAAAGATCTTCCAGGACTTAAGACGCCAGTAGGTAGAGGAAAAGCCTGCCTTCGTTTGGCATTAATGCAAAAGA
AACTTTCAAATATATGAAAGCTTTGATCAGTAAGAAAGAACTCAGTGAATTCTACGAACCCAGTGCCCTTATGATGGAAG
AAGAAGGAGCCATAATTGCTGGCCTGTTGGTGGGTCTGAATGTAACTGATGCCAATTTCTGTTGTGAAAGGAGAAGACCT
GGACTCTCAGGCTGGAGTTACAGATTTTTCAGTGTATCTCAAGGACGGGAACAGCAGTAAAGGTAGTGAAGGAGACAGTC
AGTTTACTGCGATTCTGGACCAGAAGAAATTTGTAGAAGACCTGAACAGACATTTGAATGCTACTGTAAATAACCTGCAG
GCAAAAGTAGATGCATTCGAAAAATCCAACAGTAAACTGACAGAGGAGCTTGCAGTTGCAAACACCAGAATTATTACCTT
ACAAGAAGAAATGTAGTGAGTTAAAGAGGAAAGTTCCTACATACTGGAATCCAGTTAAAAGGGTCCCAAGCAAGACAGAA
CTGCAGAAGAGCAAGCACCAAATGAAGCAAGAAAGCATTTAAAAGAAGAGACACGATTACCATTGGATGTTGAAAAAATT
GGAGATGCAGATCAGCATGAGGCAGGAGATATGAAGATGCTGGTGAAGGATGTCTGTGGGAAGCAGGATGCCCTGGTATC
TCTTCAGCAGCAGCTGGATGATCTCAGGCCCCTCAAGCATGAACTTGCCTTTAAGCTGCAGAGTTCAGACTTAGGAGTAA
AACAGAAAAGTGAACTAAATAGTAGCTTGGAAGAGAAGACTAATCAGATGGCTGCTATCATTAAACAACTTGAACAAAGA
CTGTGCCAGGCTGAGCAAAGCTGTCAGTCTGCTGAGTTGGACAACTGGCTCTTCAAACAGGACTTTGAAGATAAGATCAA
CAGCCTGCATCTGGAAGTCAAGGAGCTCACCAGGCAGCAGAACCAGCTTGAGTTAGAACTAAAACAGGAAAAAGAAAGAA
AATTACAAAACAACAGGAGTATCCCAGGAAAGGGTTCCCAGAAGCCAGAATCCAAGATGGATGGGAAGCACAAAATGCAA
GAGGAAAATATTAAACTAAAAATGCCTCTGGAAGAAAGCCACAGACTGCAACCCCACCCTATG

Alignment

ORF - retro_nleu_959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.4 %
• Parental protein coverage: 68.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVGRGRAWLRLALMQKKLS-EYMKALINKKELL
          FLGQN.SFWG.LE...................PGLKTPVGRG.A.LRLALMQKKLS..YMKALI.KKEL.
Retrocopy FLGQNISFWGALEXXXXXXXXXXXXXXXXXXXPGLKTPVGRGKACLRLALMQKKLS<KYMKALISKKEL-

Parental  SEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC-MKGEDLDSQVGVIDFSMYLKDGNSSKGTEGDGQITA
          SEFYEP.ALMMEEEGAIIAGLLVGLNV.DANFC..KGEDLDSQ.GV.DFS.YLKDGNSSKG.EGD.Q.TA
Retrocopy SEFYEPSALMMEEEGAIIAGLLVGLNVTDANFC>VKGEDLDSQAGVTDFSVYLKDGNSSKGSEGDSQFTA

Parental  ILDQKNYVEELNRHLNATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRK
          ILDQK..VE.LNRHLNATVNNLQAKVDA.EKSN.KLTEELAVAN.RIITLQEEM..VKEESSYILES..K
Retrocopy ILDQKKFVEDLNRHLNATVNNLQAKVDAFEKSNSKLTEELAVANTRIITLQEEM**VKEESSYILESS*K

Parental  GPKQDRTAEGQALSEARKHLKEETQLRLDVEKELEMQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLD
          GPKQDRTAE.QA..EARKHLKEET.L.LDVEK...........M....K....DVC.KQDALVSL.QQLD
Retrocopy GPKQDRTAEEQAPNEARKHLKEETRLPLDVEKIGDADQHEAGDMKMLVK----DVCGKQDALVSLQQQLD

Parental  DLRALKHELAFKLQEFRLRVKQKSELNSRL-EKTNQMAATINNLKSRLRQAERSRQSAELDNRLFKQDFG
          DLR.LKHELAFKLQ...L.VKQKSELNS.L.EKTNQMAA.I..L..RL.QAE.S.QSAELDN.LFKQDF.
Retrocopy DLRPLKHELAFKLQSSDLGVKQKSELNSSLEEKTNQMAAIIKQLEQRLCQAEQSCQSAELDNWLFKQDFE

Parental  DKINSLQLEVEELTRQRNQLELELKQEKERRLQNDRSIPGRGSQKSESKMDGKHKMQEENVILKKPLEES
          DKINSL.LEV.ELTRQ.NQLELELKQEKER.LQN.RSIPG.GSQK.ESKMDGKHKMQEEN..LK.PLEES
Retrocopy DKINSLHLEVKELTRQQNQLELELKQEKERKLQNNRSIPGKGSQKPESKMDGKHKMQEENIKLKMPLEES

Parental  HRLEPHPM
          HRL.PHPM
Retrocopy HRLQPHPM

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_959 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014529	1 retrocopy	retro_cjac_1829,
Nomascus leucogenys	ENSNLEG00000007716	1 retrocopy	retro_nleu_959 ,