RetrogeneDB ID: retro_nleu_1336

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397289.1:10462441..10463356(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIPIN
• Ensembl ID: ENSNLEG00000012909
• Aliases: None
• Description: TIMELESS interacting protein [Source:HGNC Symbol;Acc:30750]

Sequence

>retro_nleu_1336
ATGATAGAACCACAAGAGAATGGCATGATTGACCTACCTGATTATGAGCATGTAGAAGATGAAACTTTTCCTCTTTTCCC
ACCTGCAATCTAGCTCTAGAGAGACAAGATGATGAAGGGGCTGAACCTGATGAAGAGTCAGGAAGCAGAGCACCTGTTCC
CGTACCTCCAAAGAGAACAGTTAAAAGAAATATACTGAAGCTGGATGCTCAGAGATTAATTTCAGAGAGAGGACTTCCAG
CCTTAAGGCATGTATTTGATAAGGCAAAATTCAAAGGTAAAGGTCATGAGGCTGAAGATTTGAAGACTCTGATCAGACAC
GTGGAGCACTGGGCACATAGGCTATTCCCTAAACTGCAGTTTGAGGATTTTATTGACAGAGTTGAATACCTGGGAAATGA
AAAGGAAGTTCAGACTTGTTTAAAACAAATTCGACTTGATCTCCCTATTTTACCTGAAGATTTTATTAGCAATAATGATG
AAGTTGTGGAAAATAATGGACATGATGTAACCGCTACTGAATTAGATCCCTTTCTGACAAACTCATCTGAAAGTGAGATA
TTTGCTTCTGAGTCAAGTAGAAGCCTAACAGAAGAGCAACAACAGAAAATTGAGAGAAATAAACAAATGGCCTTAGAAAG
AAGGCAGGCAAAGCTGCTAAGTAATAGTCAGTCCCTAGGAAATGATACGTTAATGAATGCACCCAGGGCATAGACAGTTG
AGGTTAATACTTGATGAGGATCAAAAGGAGGAGTCAATTGGATTAAGGGAAGACATGCTAGACAATCCATGTAATGATGC
TCCTGCTAATACTTCAAATGAAGAGGAGGAATTAAAATTAGAGGACACACTACTGGATCAGTCTTTCACAAATGTGCAAC
AGTAACTTGAAGCTTCATCCAGAAATGTTACTGAA

Alignment

ORF - retro_nleu_1336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.74 %
• Parental protein coverage: 95. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLEPQENGTIDLPDYEHVEDET-FPPFPP-PASPERQDGEGTEPDEESGNGAPVPVPPKRTVKRNIPKLD
          M.EPQENG.IDLPDYEHVEDET.F..FP......ERQD.EG.EPDEESG..APVPVPPKRTVKRNI.KLD
Retrocopy MIEPQENGMIDLPDYEHVEDET<FSSFPTCNLALERQDDEGAEPDEESGSRAPVPVPPKRTVKRNILKLD

Parental  AQRLISERGLPALRHVFDKAKFKGKGHEAEDLKMLIRHMEHWAHRLFPKLQFEDFIDRVEYLGSKKEVQT
          AQRLISERGLPALRHVFDKAKFKGKGHEAEDLK.LIRH.EHWAHRLFPKLQFEDFIDRVEYLG..KEVQT
Retrocopy AQRLISERGLPALRHVFDKAKFKGKGHEAEDLKTLIRHVEHWAHRLFPKLQFEDFIDRVEYLGNEKEVQT

Parental  CLKRIRLDLPILHEDFVSNNDEVAENNEHDVTATELDPFLTNLSESEMFASESSRSLTEEQQQRIERNKQ
          CLK.IRLDLPIL.EDF.SNNDEV.ENN.HDVTATELDPFLTN.SESE.FASESSRSLTEEQQQ.IERNKQ
Retrocopy CLKQIRLDLPILPEDFISNNDEVVENNGHDVTATELDPFLTNSSESEIFASESSRSLTEEQQQKIERNKQ

Parental  LALERRQAKLLSNSQSLGNDMLTNTPRAHTVAEVNT-DEDQKEESNGLNEDILDNPCNDAIANTLN-EEE
          .ALERRQAKLLSNSQSLGND.L.N.PRA.TV.EVNT.DEDQKEES.GL.ED.LDNPCNDA.ANT.N.EEE
Retrocopy MALERRQAKLLSNSQSLGNDTLMNAPRA*TV-EVNT>DEDQKEESIGLREDMLDNPCNDAPANTSNEEEE

Parental  LKLEETLLDQSFKNVQQQLDATSRNITE
          LKLE.TLLDQSF.NVQQ.L.A.SRN.TE
Retrocopy LKLEDTLLDQSFTNVQQ*LEASSRNVTE

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_1336 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004860	1 retrocopy	retro_chof_223,
Dasypus novemcinctus	ENSDNOG00000003177	3 retrocopies	retro_dnov_1334, retro_dnov_1481, retro_dnov_410,
Homo sapiens	ENSG00000075131	1 retrocopy	retro_hsap_4837,
Gorilla gorilla	ENSGGOG00000000061	3 retrocopies	retro_ggor_1268, retro_ggor_2907, retro_ggor_3016,
Loxodonta africana	ENSLAFG00000026016	1 retrocopy	retro_lafr_1104,
Microcebus murinus	ENSMICG00000004386	2 retrocopies	retro_mmur_155, retro_mmur_255,
Macaca mulatta	ENSMMUG00000003695	1 retrocopy	retro_mmul_1582,
Nomascus leucogenys	ENSNLEG00000012909	1 retrocopy	retro_nleu_1336 ,
Pan troglodytes	ENSPTRG00000007192	2 retrocopies	retro_ptro_1145, retro_ptro_3220,
Rattus norvegicus	ENSRNOG00000043068	1 retrocopy	retro_rnor_364,