RetrogeneDB ID: retro_nleu_878

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397275.1:5166965..5167809(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD8
• Ensembl ID: ENSNLEG00000016876
• Aliases: None
• Description: None

Sequence

>retro_nleu_878
GTGAACAGTGCAGCCGGTGCCTTGAGCTCCGGGCCCATGGCGACCTAGGGCCCTGTCCTGCAGGCTGCAGACAGCAAGTA
CAAGCAACTCACGGGCGAGTGGAACCATAAAAGCCCCAATCTTAGCAAGTGCAGGGAAGAGCTGGGCCGCCTCGAGCTAG
TTCTTCTGGAGCTCAACTACTTGCCAACCACAGGGACCAAGCTGACCAAACAGCGGCTCATTCTGGCCCGTGACATACTG
AAGATCGGGGCCAGTGGAGCATCCTATGCAAGGACATCCCCTCCTTCAAGCGCCACATGACCCAGCTCAAATGCTGCTAC
TTTGATTGCAAGGAACAGCTTCCCCAGTCAGCCTACATGCACCAGCTCTTGGGCCTCAACCTTCTCTTCCTGCTGTCCCA
GAAGCGGGTGGCTGAGTTCCACATGGAGTTGGAGTGGCTGCCTGCCAAGGACATCCAGACCAGTGTCTACACCAAAAACC
CTGTGTCCCTGGAGCAATACCTGATGGAAGGCAGCTACAACAAAGTGTTCCTGGCCAAGGGTAACATCCCCGCCAAGAGC
TACACCTTCTTCATCGACATCCTGCTTGACACTATCAGGGATGAGATCACCGGGTGCATCGAGAAAGCCTATGAGAAAAT
CCCTTTTACCGAGGCCACCAGATCCTCTTCTTCAACACACCCAAAAAGATGACCGACTATACCAAGAAGTGAGAGTGGGT
CCTGGGCCCCAACAACTAATATAGTTTTGCCAGCCAGCAGCAGGAGCCAGAAGACACTACCATTCCCTCCACAGAACTGG
CCAAACAGGTCACCGAGTATGCCCGGCAGCTGGAGATGATCGTC

Alignment

ORF - retro_nleu_878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.56 %
• Parental protein coverage: 80.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VNGAAGFSSSGPAATSGAVLQAATGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPTTGTKLTK
          VN.AAG..SSGP.AT.G.VLQAA...Y.QL.GEWN.KSPNLSKC.EELGRL.LVLLELN.LPTTGTKLTK
Retrocopy VNSAAGALSSGPMAT*GPVLQAADSKYKQLTGEWNHKSPNLSKCREELGRLELVLLELNYLPTTGTKLTK

Parental  QQLILARDILEIGA-QWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRVAE
          Q.LILARDIL.IGA.QWSIL.KDIPSF.R.M.QLKC.YFD.KEQLP.SAYMHQLLGLNLLFLLSQ.RVAE
Retrocopy QRLILARDILKIGA<QWSILCKDIPSFKRHMTQLKCCYFDCKEQLPQSAYMHQLLGLNLLFLLSQKRVAE

Parental  FHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIEK
          FH.ELE.LPAKDIQT.VY.K.PVSLEQYLMEGSYNKVFLAKGNIPA.SYTFFIDILLDTIRDEI.GCIEK
Retrocopy FHMELEWLPAKDIQTSVYTKNPVSLEQYLMEGSYNKVFLAKGNIPAKSYTFFIDILLDTIRDEITGCIEK

Parental  AYEKILFTEATR-ILFFNTPKKMTDYAKKRGWVLGPNNYYSFASQQQKPEDTTIPSTELAKQVIEYARQL
          AYEKI.FTEATR.ILFFNTPKKMTDY.KK..WVLGPNN.YSFASQQQ.PEDTTIPSTELAKQV.EYARQL
Retrocopy AYEKIPFTEATR<ILFFNTPKKMTDYTKK*EWVLGPNN*YSFASQQQEPEDTTIPSTELAKQVTEYARQL

Parental  EMIV
          EMIV
Retrocopy EMIV

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_878 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000099341	1 retrocopy	retro_hsap_456,
Monodelphis domestica	ENSMODG00000013151	1 retrocopy	retro_mdom_58,
Nomascus leucogenys	ENSNLEG00000016876	1 retrocopy	retro_nleu_878 ,
Pongo abelii	ENSPPYG00000009931	1 retrocopy	retro_pabe_277,
Pan troglodytes	ENSPTRG00000010926	1 retrocopy	retro_ptro_343,
Ictidomys tridecemlineatus	ENSSTOG00000014464	1 retrocopy	retro_itri_10,