RetrogeneDB ID: retro_nleu_1377

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397291.1:9270848..9272459(-)
• Located in intron of: ENSNLEG00000001700

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_1377
GGGGAATCTGAAGAAGAAAGTGCAGAGACTCCTAAAGAAACAGAAAATAATGTGGAGAAGCCAGATAATGATGAAGATGA
CAGTGAGGTGACCAGCCTGCCCCTGGGACTGACAGGAGCTTTTGAGGATACTTCATTTGTTTCTCTACATAATCTTGTCA
ATGAAAACACTCTGAAGGCAATAAAGGAAATGGGTTTTACAAACATGACTGAAATTCAGCATAAAAGTATCAGACCACTT
CTGGAAGGCAGGGACTTCTAGTAGCTGCAAAAGCAGGCAGTGGTAAAACCCTGGCTTTTCTCATTCCTGCAGCTGAACTC
ATTGTTAAGTGAAAGTTCATGCCCAGGAATGGAGTGGGAGTCCTTATTCTCTCACCTACTAGAGAACTAGCCATGCAAAC
TTTTGGTGTTCTTATGGAGCTAAAGACATGCCACGTGCATACCTACGGGTTGATAATGGGTGGCAGTAACAGATCTGCTG
AAGCACAGAAACTTGCTAATGGGATCAACATCATTGTGGCCACACCAGGCCGTCTGCTGGACCATATGCAGAATACCCCC
AGGGCTTATGTATAAAAACCTGCAGTGTCTGGTTATTGATCAAGCTGATCATATCTTGGATGTTGGGTTTGCAGAGGAAT
TAAAGCAAGTTATTAAACTTTTGCCAACACGTAGACAGACTATGCTCTTTCCTGCCACCCAAACTCAAAAAGTTGAAGGC
CTGGCAAGGATTTATCTGAAAAAGGAGGCATTGTATGTTGGTGCTGACGATGATAAAGCTAATGCAACAGTGGATGGTCT
TGAGCAGGGATATGTTGTTTGTCCTTCCAAAAAGAGATTCCTTCTGCTCTTTACATTTCTTAAGAAGAATCAAAAGAAGA
AGCTTATGGTCTTCTTTTCATCTTGCATGTCCGTGAAATACCACTATGAGTTGCTGAACTACATTGATTTGCCTGACGTG
GCCATTCATGGAAAGCAAAAGCAAATTAAGTGTACAACCACATTCTTCCAGTTCTGCAACCCAGATTCAGGAACACTATT
GTGTACGGATGTGGCAGCAAGAGGACTGGACATTCCTGAAGTTGACTGGATTGTTCAGTATGACCCTCCAGATGACCCTA
AGGAATACATTCATTGTGTAGGTAGAACAGCCAGAGGCCTAAATGGGAGAGGGCATGCCCTGCTCATTTTGTGCCCAGAA
TAATTGGGTTTTCTTTGCTACTTGAAACAATCCAAGGTTCCATTAAGTTTATTAGATTTTTCCTGGTCTAAAATTTCTGA
CATTCAGTCCCAGCTTGAGAAATTGATTGAAGAGAACTACTTTCTTCATAAGTCAGCTCAGGAACCATATAAGCCGTATA
TACAAGCCTATGATTCCCATTCTCTGAAACAGATCTTTAATGTTAATAACTTAAATTTGCCTCAAGTTGCTCTGTCATTT
GGTTTCAAGGTGCCTCCCTTTGTTGATCTGAACATCAACTGCAATGAAGGCAAGCAGAAAAAGCGAGGGGGTAGTGGTGG
ATTTGGCTACCAAAAAACCAAGAAAATTGAGAAGTCCAAAATCTTTAAACACATTAGCAAGAAATCATCCGACAGCAGGC
AGTTCTCTCAC

Alignment

ORF - retro_nleu_1377 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.28 %
• Parental protein coverage: 80.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GQSEEESAETPKETENNVEKPDNDEDDSEVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKEMGFTNMT
          G.SEEESAETPKETENNVEKPDNDEDDSEV.SLPLGLTGAFEDTSF.SL.NLVNENTLKAIKEMGFTNMT
Retrocopy GESEEESAETPKETENNVEKPDNDEDDSEVTSLPLGLTGAFEDTSFVSLHNLVNENTLKAIKEMGFTNMT

Parental  EIQHKSIRPLLEGRD-LLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLK
          EIQHKSIRPLLEGRD.LL.AAK.GSGKTLAFLIPA.ELIVK..FMPRNG.GVLILSPTRELAMQTFGVL.
Retrocopy EIQHKSIRPLLEGRD<LLVAAKAGSGKTLAFLIPAAELIVK*KFMPRNGVGVLILSPTRELAMQTFGVLM

Parental  ELMTHHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTP-GFMYKNLQCLVIDEADRILDV
          EL.T.HVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTP.G.MYKNLQCLVID.AD.ILDV
Retrocopy ELKTCHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTP>GLMYKNLQCLVIDQADHILDV

Parental  GFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEK
          GF.EELKQ.IKLLPTRRQTMLF.ATQT.KVE.LARI.LKKE.LYVG.DDDKANATVDGLEQGYVVCPS.K
Retrocopy GFAEELKQVIKLLPTRRQTMLFPATQTQKVEGLARIYLKKEALYVGADDDKANATVDGLEQGYVVCPSKK

Parental  RFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLC
          RFLLLFTFLKKN.KKKLMVFFSSCMSVKYHYELLNYIDLP..AIHGKQKQ.K.TTTFFQFCN.DSGTLLC
Retrocopy RFLLLFTFLKKNQKKKLMVFFSSCMSVKYHYELLNYIDLPDVAIHGKQKQIKCTTTFFQFCNPDSGTLLC

Parental  TDVAARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSEF
          TDVAARGLDIPEVDWIVQYDPPDDPKEYIH.VGRTARGLNGRGHALLIL.PE.LGFL.YLKQSKVPLS..
Retrocopy TDVAARGLDIPEVDWIVQYDPPDDPKEYIHCVGRTARGLNGRGHALLILCPE*LGFLCYLKQSKVPLSLL

Parental  DFSWSKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFV
          DFSWSKISDIQSQLEKLIE.NYFLHKSAQE.YK.YI.AYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFV
Retrocopy DFSWSKISDIQSQLEKLIEENYFLHKSAQEPYKPYIQAYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFV

Parental  DLNVNSNEGKQKKRGGGGGFGYQKTKKVEKSKIFKHISKKSSDSRQFSH
          DLN.N.NEGKQKKRGG.GGFGYQKTKK.EKSKIFKHISKKSSDSRQFSH
Retrocopy DLNINCNEGKQKKRGGSGGFGYQKTKKIEKSKIFKHISKKSSDSRQFSH

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_1377 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,