RetrogeneDB ID: retro_nleu_1396

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397292.1:3451164..3452476(+)
• Located in intron of: ENSNLEG00000001226

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSNLEG00000011769
• Aliases: None
• Description: None

Sequence

>retro_nleu_1396
CTTTTCTCATCCCTGCAGTTGAACTCATTGTTAAATTTCATGCCCAGGAATGGAACGGGGGTCCTTATTCTCTCACCTAC
TAGAGAACTAGTCATGCAAACTTTTGGTGTTCTTAAGGAGCTAATGACTCACCACATGCATACCTATGGGTTGATAATGG
GTGGCAGTAATAGATCCACTGAAGCACAGAAACTTGCTAATGGGATCAACATCATTGTGGTCACACCAGGCTGTCTGCTG
GACCATATGCAGAATATCCCAGGGTTTATGTATAAAAATCTGCAGTGTCTGGTTATCAATGAAGCTGATCGTATCTTGGA
TGTTGAGTTCGAAGAGGAATTAAAACAAATTATTAAACTTTTGCCATCACGTAGACAGACGATGCTCTTTTCTGCCACCC
AAACTCAAAAAGTTGAAGGCCTGGCAAGGATTTCTCTGAAAAAGGAGCCATTGTATGTTGGTGTTGATGATGATAAAGCT
AATGCAACAGTGGATGGTCTTGGGCAGGGATATGTTTTTTGTCCTTCTGAAAAGAGATTCCTTCTACTCTTTACATTCCT
TAAGGAGAACCAAAAAAGGAAGCTTATGGCCTTCTTTTCATCTTGTATGTCCGTGAAATACCACTATGAGTTGCTGAACT
ACATTGATTTGCCCGTCTTGGCCATTCATGGAAAGCAAAAGCAAAATAAGCGTACAACCACATTCTTCCAGTTCTGCAAT
GCAGATTTAGGAACACTATTGTGTACAGATGTGGCAGCAAGAGAACTGGACATTACTGAAGATGACTGGATTGTTCAGTA
TGACCCTCCAGATGACCCTAAGGAATAATATTCATCGTGTGGGTAGAACAGCCAGAGGCCTAAATGGGAGAGGGCCTGCC
TTGCTCATTTTGCACCCAGAAGAATTGGGTTTTCTTCACTACTTGAAACGATCCAAGGTTCCATTAAGTAAATTTGACTT
TTCCTGGTCTAAAATTTCTGACATTCAGTCTCAGCTTGAGAAATTGATTCAAAAGAACTACTTTTTTCATAAGTCAGCTC
AGGAAGCATATAAATCATACATACAAGCCTACAATTCCCATTCTCTGAAACAGATCTTTAATGTTTAATAACTTAAATTT
GCCTCAAGTTGCTCTGTCATTGGTTTCAAGGTGCCTCCCTTTGTTGATCTGAACGTCAACAGCAATGAAGGCAAGCAGAA
AAAGTGAGTAGGCAGTGGTGGATTTGGCTACCAGAAAACCAAGAAAGTTGAGAAGTCCAAAATCTTTAAACACATTAGCA
AGCAAGCATCCAACAGCAGGCAGTTCTGTCAC

Alignment

ORF - retro_nleu_1396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.41 %
• Parental protein coverage: 65.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGIN
          L.....L...L.FMPRNGTGVLILSPTREL.MQTFGVLKELMTHH.HTYGLIMGGSNRS.EAQKLANGIN
Retrocopy LFSSLQLNSLLNFMPRNGTGVLILSPTRELVMQTFGVLKELMTHHMHTYGLIMGGSNRSTEAQKLANGIN

Parental  IIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVED
          IIV.TPG.LLDHMQN.PGFMYKNLQCLVI.EADRILDV.FEEELKQIIKLLP.RRQTMLFSATQT.KVE.
Retrocopy IIVVTPGCLLDHMQNIPGFMYKNLQCLVINEADRILDVEFEEELKQIIKLLPSRRQTMLFSATQTQKVEG

Parental  LARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYE
          LARISLKKEPLYVGVDDDKANATVDGL.QGYV.CPSEKRFLLLFTFLK.N.K.KLM.FFSSCMSVKYHYE
Retrocopy LARISLKKEPLYVGVDDDKANATVDGLGQGYVFCPSEKRFLLLFTFLKENQKRKLMAFFSSCMSVKYHYE

Parental  LLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARGLDIPEVDWIVQYDPPDDPKE-YIHR
          LLNYIDLPVLAIHGKQKQNKRTTTFFQFCNAD.GTLLCTDVAAR.LDI.E.DWIVQYDPPDDPKE..IHR
Retrocopy LLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADLGTLLCTDVAARELDITEDDWIVQYDPPDDPKE>NIHR

Parental  VGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKNYFLHKSAQEA
          VGRTARGLNGRG.ALLIL.PEELGFL.YLK.SKVPLS.FDFSWSKISDIQSQLEKLI.KNYF.HKSAQEA
Retrocopy VGRTARGLNGRGPALLILHPEELGFLHYLKRSKVPLSKFDFSWSKISDIQSQLEKLIQKNYFFHKSAQEA

Parental  YKSYIRAYDSHSLKQIFNV-NNLNLPQVALS-FGFKVPPFVDLNVNSNEGKQKKRGGGGGFGYQKTKKVE
          YKSYI.AY.SHSLKQIFNV.NNLNLPQVALS..GFKVPPFVDLNVNSNEGKQKK..G.GGFGYQKTKKVE
Retrocopy YKSYIQAYNSHSLKQIFNV>NNLNLPQVALS<IGFKVPPFVDLNVNSNEGKQKK*VGSGGFGYQKTKKVE

Parental  KSKIFKHISKKSSDSRQFSH
          KSKIFKHISK..S.SRQF.H
Retrocopy KSKIFKHISKQASNSRQFCH

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_1396 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 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000017166	2 retrocopies	retro_etel_1919, retro_etel_297,
Homo sapiens	ENSG00000088205	6 retrocopies	retro_hsap_1361, retro_hsap_1579, retro_hsap_3223, retro_hsap_3561, retro_hsap_608, retro_hsap_834,
Gorilla gorilla	ENSGGOG00000028420	4 retrocopies	retro_ggor_1201, retro_ggor_2189, retro_ggor_2402, retro_ggor_535,
Microcebus murinus	ENSMICG00000017590	1 retrocopy	retro_mmur_1560,
Myotis lucifugus	ENSMLUG00000017607	1 retrocopy	retro_mluc_2279,
Macaca mulatta	ENSMMUG00000021343	1 retrocopy	retro_mmul_2192,
Monodelphis domestica	ENSMODG00000000533	1 retrocopy	retro_mdom_414,
Nomascus leucogenys	ENSNLEG00000011769	4 retrocopies	retro_nleu_1377, retro_nleu_1396 , retro_nleu_266, retro_nleu_437,
Pongo abelii	ENSPPYG00000012796	4 retrocopies	retro_pabe_1128, retro_pabe_1301, retro_pabe_2670, retro_pabe_744,
Pan troglodytes	ENSPTRG00000012391	5 retrocopies	retro_ptro_1064, retro_ptro_2174, retro_ptro_2419, retro_ptro_448, retro_ptro_933,