RetrogeneDB ID: retro_nleu_533

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397267.1:1594958..1595859(+)
• Located in intron of: ENSNLEG00000000611

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRIX1
• Ensembl ID: ENSNLEG00000014452
• Aliases: None
• Description: None

Sequence

>retro_nleu_533
ATGGCGGCAACCAAGAGGAAACAGCATGGAGGCGTGGCAGTTCAGGCGAAGAACCCAAAAAGAAGCGAAAAAGAGGCCGA
GCGGCCAGCTAAGCTGGGCGCCACCGCAGAGGAGGTGGAAAAAGACAGAGACTGGATTCCAGGCCCCGTTTGCAAGGGGG
AGTGAAAAAACAAGGAATGGATTTTCATCTTTTCTTCCAGAGGAATAAATAAATTTTAGAACAAGACATTTTATGCAGGA
CTTGAGAATGTTGATGCCTCATTCTAAAGTAGATACTAAAATGGATCGTAAGCATAAATAATTTGAGATTAGTGAGTTCT
GTGAAATGAAAAACTGTAATAAATGCATCTACTTTGAAGCTAAGAAAAAACAGGATCTCTTTATGTAGCTTTCAAATTCA
CCTCATGGACCATCTGCTAAATGCCTTGTTCAAAATATTCATACCCTAGCTGAATTAAAGATGACTGGAAACCTTTTGAA
AGGTTCTTGCCCCTTTTGTCTTGACCCAGCTTTTGATGAATTACTACATTATGCTGTGTTAAAAGAACTCTTAATTCAGA
TCTTTAGTACACCGTGGCATCATCCCAAAAGCCAACCATTCATGGGCCATGTGTTTACTTTCACCATTTTGGATAACAGG
ATATGGTTTCAGAAGTTTCATATCATAGAAGAAGTTGTTGCTCTTGTAGAAATAGGACCTTGTTTTGTCTTAAATCTCAT
AAACATTATTCAGGGAAGTTCTGGAGGACCAACTTTATATGAAAATTCTCACTACCAGGCACCAAAAATGCATTGCCATG
TCATAAGATCCATCACACCTGCAAAATACAGAGAGAATCAGTAAGTGAAAGATGTGCAGAAACTGAGAAAGAAAGAGCCA
AAGATACTTATTCCACATGAT

Alignment

ORF - retro_nleu_533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.28 %
• Parental protein coverage: 85.27 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAATKRKRRGDFAVQAKKPKSNEKDAEPPAKRHATAEEVEEEERDRIPG-PVCKGKWKNKERILIFSSRG
          MAATKRK..G..AVQAK.PK..EK.AE.PAK..ATAEEVE...RD.IPG.P...G..K.......F....
Retrocopy MAATKRKQHGGVAVQAKNPKRSEKEAERPAKLGATAEEVEKD-RDWIPG>PFARGSEKTRNGFSSFLPEE

Parental  -INFRTRHLMQDLRMLMPHSKAGAFMSYTLEISIYKQVCEMKNCNKCIYFEAKKKQDLYMWLSNSPHGPS
          .INFRTRH.MQDLRMLMPHSK....M............CEMKNCNKCIYFEAKKKQDL.M.LSNSPHGPS
Retrocopy *INFRTRHFMQDLRMLMPHSKVDTKMDRKHK*FEISEFCEMKNCNKCIYFEAKKKQDLFM*LSNSPHGPS

Parental  AKFLVQNIHTLAELKMTGNCLKGSRPLLSFDPAFDELPHYALLKELLIQIFSTPRYHPKSQPFVDHVFTF
          AK.LVQNIHTLAELKMTGN.LKGS.P....DPAFDEL.HYA.LKELLIQIFSTP..HPKSQPF..HVFTF
Retrocopy AKCLVQNIHTLAELKMTGNLLKGSCPFC-LDPAFDELLHYAVLKELLIQIFSTPWHHPKSQPFMGHVFTF

Parental  TILDNRIWFRNFQIIEEDAALVEIGPRFVLNLIKIFQGSFGGPTLYENPHYQSPNMHRRVIRSITAAKYR
          TILDNRIWF..F.IIEE..ALVEIGP.FVLNLI.I.QGS.GGPTLYEN.HYQ.P.MH..VIRSIT.AKYR
Retrocopy TILDNRIWFQKFHIIEEVVALVEIGPCFVLNLINIIQGSSGGPTLYENSHYQAPKMHCHVIRSITPAKYR

Parental  EKQQVKDVQKLRKKEPKTLLPHD
          E.Q.VKDVQKLRKKEPK.L.PHD
Retrocopy ENQ*VKDVQKLRKKEPKILIPHD

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_533 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 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001790	2 retrocopies	retro_chof_1664, retro_chof_1776,
Callithrix jacchus	ENSCJAG00000018506	1 retrocopy	retro_cjac_1389,
Homo sapiens	ENSG00000113460	1 retrocopy	retro_hsap_3954,
Gorilla gorilla	ENSGGOG00000004225	1 retrocopy	retro_ggor_2657,
Loxodonta africana	ENSLAFG00000007249	1 retrocopy	retro_lafr_1116,
Myotis lucifugus	ENSMLUG00000029255	3 retrocopies	retro_mluc_1402, retro_mluc_707, retro_mluc_963,
Macaca mulatta	ENSMMUG00000000442	1 retrocopy	retro_mmul_2289,
Monodelphis domestica	ENSMODG00000020386	1 retrocopy	retro_mdom_1032,
Nomascus leucogenys	ENSNLEG00000014452	1 retrocopy	retro_nleu_533 ,
Otolemur garnettii	ENSOGAG00000014827	2 retrocopies	retro_ogar_3116, retro_ogar_793,
Pongo abelii	ENSPPYG00000015390	2 retrocopies	retro_pabe_3258, retro_pabe_3379,
Pan troglodytes	ENSPTRG00000016784	1 retrocopy	retro_ptro_2684,
Rattus norvegicus	ENSRNOG00000018021	1 retrocopy	retro_rnor_1140,
Tupaia belangeri	ENSTBEG00000011652	9 retrocopies	retro_tbel_1963, retro_tbel_1964, retro_tbel_2981, retro_tbel_3002, retro_tbel_3082, retro_tbel_4194, retro_tbel_4229, retro_tbel_4418, retro_tbel_954,