RetrogeneDB ID: retro_nleu_2480

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397359.1:5986407..5987475(-)
• Located in intron of: ENSNLEG00000008897

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDSS1
• Ensembl ID: ENSNLEG00000016836
• Aliases: None
• Description: None

Sequence

>retro_nleu_2480
CCCTATTTTAATCTTGTGAAGCATTTAACACCTGCCTGTCCAAATGTATATAGTATATCACAGTTTCATCACACAACCCC
GTACAGCAAAACACACACTGGTGAGAAATACACCGATCCTTTCAAACTCGGTTGGAGAGACTTGAAAGGTCTGTATGAGG
ACATTAGAAAGGTACTGCTCATATCGACAACAGAACTTAAGGAAATGTCTGAGTACTACTTTGATGTAAAAGGAAAAGCC
TTTTGACCAATTATTGTGGTACTAATGGCCCAAGCACGTAATATTCATCATAATAACTCCCGACATGTGCAAGCTAGCCA
GCGCGCCACAGCCTTAATTGCAGGAATGATCCACACTGCTAGTCTTGTTCACGATGACGTTACTGATGATGCAAGTTCTC
GAAAAGGAAAACACAAGATCTGGGGTGAAAAGAAGGCTGTCCTTGCTGGAGATTTAATTCTTTCTGTAGTATCTATAGCT
GGGGCACAAATTGGAAATGCAACTGATATATCTATTTTAACCCAAGTTATTGAAGATTTGGTGTGTGGTGAATTTCTTCA
GCTCGGATCAAAAGAAAATGAGAATGAAAGATTTGCACAATACCTTGAAAAGACCTTCAAGAACACTGCGAGCCTGATAG
CCAGCAGTGGTAAAGCAGTCTCTGTTCTAGGATGCCCCGACCCAGTGGTGCATGAGATCGGCTATCAGTACGGAAAAAAT
GTAGGAATAGCTTTTCAGCTAATAGATGATGTATTGGACTTCACCTCATGTTCTAACATAGGCAAACCAACATCAGCTGA
TGTGAATCTCGGGTTAGCCACTGGTCCTGTCCTGTCTGCCTGTCAGCAGTTCCCAGAAATGAATGCTATGATCATGAGAT
GGTTCAGTTTGCCGGGAGATGTAGACAGAGCTCCACAGTATGTATTACAGACTGATGGTGTGCAACAAACAACCTACCTC
GCCCAGCAGTACTGCTGTGAAGCAGTAAGAGAGATCAGTAAACTTCCACCATCCCCAGAAAGAGACGCCCTCATTCAACT
TTCAGAAATCGTACTCACAAGACATAAA

Alignment

ORF - retro_nleu_2480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.94 %
• Parental protein coverage: 95.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PYINVVKHLTSACPNVYSISRFHHTTPDSKTHSGEKYTDPFKLGWRDLKGLYEDIRKELLISTSELKEMS
          PY.N.VKHLT.ACPNVYSIS.FHHTTP.SKTH.GEKYTDPFKLGWRDLKGLYEDIRK.LLIST.ELKEMS
Retrocopy PYFNLVKHLTPACPNVYSISQFHHTTPYSKTHTGEKYTDPFKLGWRDLKGLYEDIRKVLLISTTELKEMS

Parental  EYYFDGKGKAFRPIIVALMARACNIHHNNSRHVQASQRTIALIAEMIHTASLVHDDVIDDASSRRGKHTV
          EYYFD.KGKAF.PIIV.LMA.A.NIHHNNSRHVQASQR..ALIA.MIHTASLVHDDV.DDASSR.GKH..
Retrocopy EYYFDVKGKAF*PIIVVLMAQARNIHHNNSRHVQASQRATALIAGMIHTASLVHDDVTDDASSRKGKH--

Parental  NKIWGEKKAVLAGDLILSAASIALARIGNTTVISILTQVIEDLVRGEFLQLGSKENESERFAHYLEKTFK
          .KIWGEKKAVLAGDLILS..SIA.A.IGN.T.ISILTQVIEDLV.GEFLQLGSKENE.ERFA.YLEKTFK
Retrocopy -KIWGEKKAVLAGDLILSVVSIAGAQIGNATDISILTQVIEDLVCGEFLQLGSKENENERFAQYLEKTFK

Parental  KTASLIANSCKAVSVLGCPDPVVHEIAYQYGKNVGIAFQLIDDVLDFTSCSDQMGKPTSADLKLGLATGP
          .TASLIA.S.KAVSVLGCPDPVVHEI.YQYGKNVGIAFQLIDDVLDFTSCS...GKPTSAD..LGLATGP
Retrocopy NTASLIASSGKAVSVLGCPDPVVHEIGYQYGKNVGIAFQLIDDVLDFTSCSN-IGKPTSADVNLGLATGP

Parental  VLFACQQFPEMNAMIMRRFSLPGDVDRARQYVLQSDGVQQTTYLAQQYCHEAIREISKLRPSPERDALIQ
          VL.ACQQFPEMNAMIMR.FSLPGDVDRA.QYVLQ.DGVQQTTYLAQQYC.EA.REISKL.PSPERDALIQ
Retrocopy VLSACQQFPEMNAMIMRWFSLPGDVDRAPQYVLQTDGVQQTTYLAQQYCCEAVREISKLPPSPERDALIQ

Parental  LSEIVLTRDK
          LSEIVLTR.K
Retrocopy LSEIVLTRHK

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_2480 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004695	1 retrocopy	retro_cjac_831,
Macaca mulatta	ENSMMUG00000005076	1 retrocopy	retro_mmul_1157,
Nomascus leucogenys	ENSNLEG00000016836	1 retrocopy	retro_nleu_2480 ,
Pan troglodytes	ENSPTRG00000002374	1 retrocopy	retro_ptro_2869,