RetrogeneDB ID: retro_nleu_437

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397265.1:24557294..24558666(+)
• Located in intron of: None

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_437
ATCAGACCACTTCTAGAAGGCAGGGATCTTCTAGCAGCTGTAAAAACAGGCAGTGGTAAAACCTTGGCTTTTCTCATCTC
TGCGATTGAACTCATTGTTAAGTTAAAGTTCATGCCCAGGAATGGAACAGGGGTCCTTATTCTGTCACCTACTAGACAAC
TAGCCATGCAAACTTTTGGTGTTCTTAAGGAGCTAATGACTCACCATGTGCACATCTATGGGTTGATAACAGGTGGCAGT
AACAGATCTGCTGAAGCACAGAAACTTGCTAACGGGATCAACATCATTGTGGTCACACCAGGCCGTCTGCTGGACCATAT
GCAGAATACCCTAGGGTTTATGTATAAAAACCTGCAGGGTCTGGCTATTGATGAAGCTGATTGTATCTTGGACGTTGGGT
TTGAAGATAAATTAAAGCAAATTATTAAACTTTTGCCAACACGCAGACAGACTATGCTCTTTTCTGCCACCTAAACTCAA
AAAGTTGAGGACCTGGCAACGATTTCTCTGAAAAAGGAGCCATTGTACGTTGGTGTTGATGATAATAAAGCTAATGCAAC
AGTGGATGGTCTTGAGCAGGGATACATTGTTTGTCCCTCTGAAAAGAGATTCCTTCTGCCCTTTACATTCCTTAAGAAGA
ACCGAAAGAAGAAGCTCACGGTCTTCTTTATATCTTGTATGTCTGTGAAATACCCTTACGGGTTGCTGAACTACATTGAT
TTGCTGTCTTGGCCATTCATGGAAAGCAAAAGCAAAATAAGCATACAACCACATTCTTCTAGTTCTGCAACGCAGATTCA
GGAACACTATTGTGTAAGGATGTGGCAGCAAGAGGACTGGACATTCCTGAAGTCGACTGGATTGTTCAGTATGACCCTCC
AGATGACCCTAAGGAATGTATTCATTGTGTGAGGAGAACAGCCAGAGGCCTAAATGGGGGAAGGCATGCCTTGCTCATTT
TGCACCCAGAAGAATTGGGTTTCCTTCACTACTTGAAACAAACCAAGGTTCCATTAAGTGAATTTGACTTTTCCTGGTCT
AAAATTTCTGACATTCAGTCTCAGCTTGAGAAACTGACTGAAAAGAACTACTTTCTTCATAAGTCAGCCCAGGAAGCATA
TAAGTCATACATACGAGCCTAGGATTCCTATTCTCTGAAACAGATCTTTAATGTTAATAACTTAAATTTGCCTCACATTG
CTCTGTCATTTGGTTTCAAGGTGCCTGCCTTTGTTGATCTGAACATGAACAGCAATGAAGGCAAGCAGAAAAAGCAAGGA
GGATTTGGCTATCAGAAAACCAAGAAAGTTGAGAAGTCCATAATCTTTAAACACATTAGCAAAAAGTCATCTGCAGCAGG
CAGTTCCCTCAC

Alignment

ORF - retro_nleu_437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.77 %
• Parental protein coverage: 68.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHV
          IRPLLEGRDLLAA.KTGSGKTLAFLI.A.ELIVKL.FMPRNGTGVLILSPTR.LAMQTFGVLKELMTHHV
Retrocopy IRPLLEGRDLLAAVKTGSGKTLAFLISAIELIVKLKFMPRNGTGVLILSPTRQLAMQTFGVLKELMTHHV

Parental  HTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQ
          H.YGLI.GGSNRSAEAQKLANGINIIV.TPGRLLDHMQNT.GFMYKNLQ.L.IDEAD.ILDVGFE..LKQ
Retrocopy HIYGLITGGSNRSAEAQKLANGINIIVVTPGRLLDHMQNTLGFMYKNLQGLAIDEADCILDVGFEDKLKQ

Parental  IIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTF
          IIKLLPTRRQTMLFSAT.T.KVEDLA.ISLKKEPLYVGVDD.KANATVDGLEQGY.VCPSEKRFLL.FTF
Retrocopy IIKLLPTRRQTMLFSAT*TQKVEDLATISLKKEPLYVGVDDNKANATVDGLEQGYIVCPSEKRFLLPFTF

Parental  LKKNRKKKLMVFFSSCMSVKYHYELLNYIDL-PVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARG
          LKKNRKKKL.VFF.SCMSVKY.Y.LLNYIDL..VLAIHGKQKQNK.TTTFF.FCNADSGTLLC.DVAARG
Retrocopy LKKNRKKKLTVFFISCMSVKYPYGLLNYIDL<AVLAIHGKQKQNKHTTTFF*FCNADSGTLLCKDVAARG

Parental  LDIPEVDWIVQYDPPDDPKEYIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSEFDFSWSKI
          LDIPEVDWIVQYDPPDDPKE.IH.V.RTARGLNG..HALLIL.PEELGFL.YLKQ.KVPLSEFDFSWSKI
Retrocopy LDIPEVDWIVQYDPPDDPKECIHCVRRTARGLNGGRHALLILHPEELGFLHYLKQTKVPLSEFDFSWSKI

Parental  SDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFVDLNVNSN
          SDIQSQLEKL.EKNYFLHKSAQEAYKSYIRA.DS.SLKQIFNVNNLNLP..ALSFGFKVP.FVDLN.NSN
Retrocopy SDIQSQLEKLTEKNYFLHKSAQEAYKSYIRA*DSYSLKQIFNVNNLNLPHIALSFGFKVPAFVDLNMNSN

Parental  EGKQKKRGGGGGFGYQKTKKVEKSKIFKHISKKSSD-SRQFSH
          EGKQKK.GG...FGYQKTKKVEKS.IFKHISKKSS..SRQF.H
Retrocopy EGKQKKQGG---FGYQKTKKVEKSIIFKHISKKSSA<SRQFPH

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_437 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,