RetrogeneDB ID: retro_nleu_1300

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397288.1:11834859..11835995(+)
• Located in intron of: ENSNLEG00000015647

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX50
• Ensembl ID: ENSNLEG00000011631
• Aliases: None
• Description: None

Sequence

>retro_nleu_1300
AAGATTGATGTTGTTGGAAAAATGACTCAAAAGGCTGCAGCTACTGTGGAACATTTGCCCATCCAGTGTCATTGGTCTCA
GAGGCCAGCATTTATTGGAGATGTCCTTCAAGTCTACAGTGGGTCTGAAGGGAGGGCTATTATTTTCTGTGAGACCAAGA
GGAGTGTAACTGAAATGACCATGAATCCACACATAAAATAGAATGCCCAGTGTTTACATGGGGACATTGCACAGTCACAA
AGAGAAACTACACTAAAAGGCTTCAGAGAAGGTAGTTTTAAAGTTTTGGTGGCAACCAACGTGGCTGCCTGTGGTTTGGA
CATTCCTGAAGTTGACCTGGTGATTCAAAATTCTCCTCAGGATGTTGAGTCTATATCCATCGTTCTGGACGCACAGGTAG
AGCTGGACGGACAGGGATTTGTATATGTTTTTATCAACCAAGAGAAAGAGGTCAACTAAGATATGTGGAACAAAAAGCAG
GAATTACTTTTAAATGTGTAGGTGTTCCTTCTACAATGGATTTAGTTAAATCTAAAAGCATGGGTGCCATAAGGTCTCTG
GCTTCTGTTTCTTATGCTGCTGTTGATTTTTTCCAACCATCAGCTCAGATACTGATAGAAGAGAAAGGGGCAGTGGATGC
ATTGGCTGCAGCTTTAGCCCACATTTCTGGTGCATCAAGCTTTGAACCACGATCTTTGATCACCTCTGATAAGGGATTTG
TGACCATGACTCTGGAAAGCCTAGAGGAAATACAGGATGTCAGCTGTGCTTGGAAAGAACTTAATGGAAAGCTGAGTCGT
AATGCAGTGTCTCAGATTACCAGAATGTGCCTCTTGAAAGGAAATGTGGGTGTTTGCTTTGATGTTCCTACAACTAAGTC
AGAAAGGTTACAGGCAGAGTGGCATGATTCCAACTGGATATTCTCAGTGCCAGCCAAATTACCTGAAATTGAAGAATATT
ATGATGGAAACACATCTTCTAATTCCAGACAGAGGAGCGGTTGGTCAAGTGGCCAGTTGGGCCGATCAAGTGGTGGATCT
GGCAGCCGGTCAGTGAGACAGAGTCCACAAGGGAGTCGCTCAGGAAGTCGACAAGATGGTAGAAGATGAAGTGGGAATAG
AAATCGATCAAGAAGT

Alignment

ORF - retro_nleu_1300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.15 %
• Parental protein coverage: 51.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQ
          ..D.VGKMTQKAA.TVEHL.IQCHWSQRPA.IGDVLQVYSGSEGRAIIFCETK..VTEM.MNPHIK.NAQ
Retrocopy KIDVVGKMTQKAAATVEHLPIQCHWSQRPAFIGDVLQVYSGSEGRAIIFCETKRSVTEMTMNPHIK*NAQ

Parental  CLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVES-YIHRSGRTGRAGRT
          CLHGDIAQSQRE.TLKGFREGSFKVLVATNVAA.GLDIPEVDLVIQ.SP.QDVES.YIHRSGRTGRAGRT
Retrocopy CLHGDIAQSQRETTLKGFREGSFKVLVATNVAACGLDIPEVDLVIQNSP-QDVES<YIHRSGRTGRAGRT

Parental  GICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEE
          GICICFYQPRERGQLRYVEQKAGITFK.VGVPSTMDLVKSKSM.AIRSLASVSYAAVDFF.PSAQ.LIEE
Retrocopy GICICFYQPRERGQLRYVEQKAGITFKCVGVPSTMDLVKSKSMGAIRSLASVSYAAVDFFQPSAQILIEE

Parental  KGAVDALAAALAHISGASSFEPRSLITSDKGFVTMTLESLEEIQDVSCAWKELNRKLSSNAVSQITRMCL
          KGAVDALAAALAHISGASSFEPRSLITSDKGFVTMTLESLEEIQDVSCAWKELN.KLS.NAVSQITRMCL
Retrocopy KGAVDALAAALAHISGASSFEPRSLITSDKGFVTMTLESLEEIQDVSCAWKELNGKLSRNAVSQITRMCL

Parental  LKGNMGVCFDVPTTESERLQAEWHDSDWILSVPAKLPEIEEYYDGNTSSNSRQRSGWSSGRSGRSGRSGG
          LKGN.GVCFDVPTT.SERLQAEWHDS.WI.SVPAKLPEIEEYYDGNTSSNSRQRSGWSSG..GRS..SGG
Retrocopy LKGNVGVCFDVPTTKSERLQAEWHDSNWIFSVPAKLPEIEEYYDGNTSSNSRQRSGWSSGQLGRS--SGG

Parental  RSGGRSGRQSRQGSRSGSRQDGRRRSGNRNRSRS
          .SG.RS.RQS.QGSRSGSRQDGRR.SGNRNRSRS
Retrocopy -SGSRSVRQSPQGSRSGSRQDGRR*SGNRNRSRS

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_1300 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018844	1 retrocopy	retro_cjac_1298,
Homo sapiens	ENSG00000107625	2 retrocopies	retro_hsap_2089, retro_hsap_2866,
Macaca mulatta	ENSMMUG00000001006	1 retrocopy	retro_mmul_982,
Mus musculus	ENSMUSG00000020076	1 retrocopy	retro_mmus_3362,
Nomascus leucogenys	ENSNLEG00000001209	1 retrocopy	retro_nleu_1094,
Nomascus leucogenys	ENSNLEG00000011631	2 retrocopies	retro_nleu_1300 , retro_nleu_609,
Otolemur garnettii	ENSOGAG00000001844	2 retrocopies	retro_ogar_1492, retro_ogar_555,
Pongo abelii	ENSPPYG00000002390	3 retrocopies	retro_pabe_2007, retro_pabe_2369, retro_pabe_2418,
Pan troglodytes	ENSPTRG00000002562	2 retrocopies	retro_ptro_1536, retro_ptro_1938,