RetrogeneDB ID: retro_nleu_2043

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397324.1:584977..585636(-)
• Located in intron of: ENSNLEG00000001288

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAUS1
• Ensembl ID: ENSNLEG00000011216
• Aliases: None
• Description: None

Sequence

>retro_nleu_2043
AGACAGAAAGCAAGTGAATATGAATCAGAAGCCAAGCCTCTTCAAGACCTTCTCATGGAGAGTGTGAATTTCTCCCTTGC
CAATCTCTCCAGCACTGGCTCCAGGTATCTGAATGCTTTGGTTGAGAGCACATGGCCCTTGAAACTAAAGATACCTCACT
AGCTAGGTTTATCCCTGCAGTGAATAATTCAACATCTGATCTTTTCAAACAAAATCCCAAACTAAAGAAATCAAGATTGA
ATGGGAAGATCTTGAAAAAAAATCTAGCCACAACATTAGTATTAGAAAAATGTCAACAAGAGGATCTCAAGAAAGTAGAG
TTTCCTTTGTCTTTGGAAAGGGTCAAAGTCAACGGTCATCTTCAGAACAGGGATGTTCTACAAGCAAAGTCAGAGAAGTT
CAGATTTGAAATCAAAGCTGCAGAGGAGCCACTTTCAGCCAGAGGCATGGATGCTTCTTCTCCATTTCATCAGTCCCTAG
TAGCGGTATCAGAGAAACTGGCAGAGTTAAAACGACAGACCATACCTTTGAAGAAAAAAATGGAGTTCTATTTAGATTTA
ATGCTGAATCCATCTCTTGCTCAAGTGAAAATTGAAGAAGCAAAGAGAGAATTAGGTAGAACTGAAGCTGAACTTACAAA
GAAAGTAGACACAATGGAA

Alignment

ORF - retro_nleu_2043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.89 %
• Parental protein coverage: 78.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KQKASEYESEAKYLQDLLMESVNFSPANVSSTGSRYLNALVDSA-VALETKDTSLASFIPAVNDLTSDLF
          .QKASEYESEAK.LQDLLMESVNFS.AN.SSTGSRYLNALV.S...ALETKDTSLA.FIPAVN..TSDLF
Retrocopy RQKASEYESEAKPLQDLLMESVNFSLANLSSTGSRYLNALVEST<MALETKDTSLARFIPAVNNSTSDLF

Parental  R-TKSKSEEIKIELEK-LEKNLTATLVLEKCLQEDIKKAELHLSTERAKVDNRRQNMDFLKAKSEEFRFG
          ..TKS...EIKIE.E..L...L..TLVLEKC.QED.KK.E..LS.ER.KV....QN.D.L.AKSE.FRF.
Retrocopy K<TKSQTKEIKIEWED>LXXXLATTLVLEKCQQEDLKKVEFPLSLERVKVNGHLQNRDVLQAKSEKFRFE

Parental  IKAAEEQLSARGMDASLS-HQSLVALSEKLARLKQQTIPLKKKLESYLDLMPNPSLAQVKIEEAKRELDS
          IKAAEE.LSARGMDAS...HQSLVA.SEKLA.LK.QTIPLKKK.E.YLDLM.NPSLAQVKIEEAKREL..
Retrocopy IKAAEEPLSARGMDASSPFHQSLVAVSEKLAELKRQTIPLKKKMEFYLDLMLNPSLAQVKIEEAKRELGR

Parental  IEAELTRRVDMME
          .EAELT..VD.ME
Retrocopy TEAELTKKVDTME

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_2043 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 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001139	3 retrocopies	retro_chof_237, retro_chof_2496, retro_chof_255,
Homo sapiens	ENSG00000152240	3 retrocopies	retro_hsap_3247, retro_hsap_4075, retro_hsap_4655,
Gorilla gorilla	ENSGGOG00000010098	2 retrocopies	retro_ggor_2210, retro_ggor_2888,
Loxodonta africana	ENSLAFG00000010897	1 retrocopy	retro_lafr_1063,
Macaca mulatta	ENSMMUG00000003124	2 retrocopies	retro_mmul_2043, retro_mmul_2476,
Monodelphis domestica	ENSMODG00000003208	1 retrocopy	retro_mdom_743,
Nomascus leucogenys	ENSNLEG00000011216	3 retrocopies	retro_nleu_1091, retro_nleu_1698, retro_nleu_2043 ,
Pongo abelii	ENSPPYG00000009131	3 retrocopies	retro_pabe_2693, retro_pabe_3344, retro_pabe_3615,
Pan troglodytes	ENSPTRG00000009992	3 retrocopies	retro_ptro_2195, retro_ptro_2762, retro_ptro_3092,
Tupaia belangeri	ENSTBEG00000010911	4 retrocopies	retro_tbel_1209, retro_tbel_1348, retro_tbel_3868, retro_tbel_4672,