RetrogeneDB ID: retro_nleu_266

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397262.1:63908019..63909326(+)
• Located in intron of: ENSNLEG00000007491

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_266
TGGCTTTTCTCAAACCTGCAGTTGAACTCATTGTTATAATTCATGCCCAGGAATGCATCAGGAGTCCTTGTTCTCTCACC
TACTAGAGAATTAGCCAAGCAAATTTTTGGTGTTCTTAAGGAGCTAATGACTCACCACGTGCATACCTATGGGTTGATAA
TGGGTGGCAGTAACAGATCTGCTGAAGCACAGAAACTTGCTAATGGGATCAACATTATTGTGGCCACACCAGGCCGTCTG
CTGTACCATATGCAGAATATCCCAGGGTTTATATATAAAAACCTGCAGTGTCTGGTTATTGATGAAGCTGATCATATCTT
GGATGTTGGGTGTGAAGAGGAATTAAAGCAAATTATTAAACTTTTGCCAACACGTAGACAGACTATGCTCTTTTCTGCCA
CCCAAACTCGAAAAGTTGAAGGCCTGGCAAGGATTTCTCTGAAAAAGGAGCCATTGTATGTTGGTGCTGATGATGATAAA
GCTAATGCAACAGTGGATGGTCTTGAGCAGGGGTATGTTGTTTGTCCTTCTGAAAAGTGATTCCTTTTGCTCTTTACATT
CCTTAAGAAGAACCGAAAGAAGAAGCTCGTGGTCTTCTTTTCATCTTGTATGTCTGTGAAATACCACTATGAGTTGCCGA
ACTGCAATGATTTGCCTGTCTTGGCCATTCATGGAAAGCAAAAGCACAATAAACGTACAACCACATTCTTCCAGTTCTGC
AACGCAGATTCAGGAACACTATCGTGTAAGGATGTGGTGGCAAGAGGACTGGACATTCCTCAAGCTGACTGGATTGTTCA
CTATGACCATCTGGATGACCTTAAGGAATATATTCATCGTGTAGGTAGAACAGCCAGAGGCCTAAATGGGAGAAGACATG
TCTTGCCCATTTTGGGCCCAGAAGATTGGGTTTTCTTCTACTTGAAACAATCCAAGATTCCATTAAGTGAATTTGACTTT
TCCTGGTCTAAAATTTCTGACATTCAGTCTCAGCTTGAGAAATTGATTGAAAAGAACTACTTTCTTTCTACGTCAGCCCA
GGAAGCATGTAAGTCATACATACCAGGTTATGATTCCCATTCTCTGAAACAGATCTTTAATTAAATAACTTAAATTTGCC
TCAAGTTGCTCTGCCATTTGGTTTCAAAATGCCTGCCTTTGTTGATCTGAATGTCAACAGCAATGAAGGCAAGTAGAAAA
AGCGAGGAGGTAGTGGTGGATTTGACTACCAGAAAACCAAGAAAGTTGAGAAGTCCAAAATCTTTAAACACATTAGTAAG
AAATCATCCAACAGCAGGCAGCTCTCA

Alignment

ORF - retro_nleu_266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.84 %
• Parental protein coverage: 65.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGI
          .L.....L...L.FMPRN..GVL.LSPTRELA.Q.FGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGI
Retrocopy WLFSNLQLNSLL*FMPRNASGVLVLSPTRELAKQIFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGI

Parental  NIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVE
          NIIVATPGRLL.HMQN.PGF.YKNLQCLVIDEAD.ILDVG.EEELKQIIKLLPTRRQTMLFSATQTRKVE
Retrocopy NIIVATPGRLLYHMQNIPGFIYKNLQCLVIDEADHILDVGCEEELKQIIKLLPTRRQTMLFSATQTRKVE

Parental  DLARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHY
          .LARISLKKEPLYVG.DDDKANATVDGLEQGYVVCPSEK.FLLLFTFLKKNRKKKL.VFFSSCMSVKYHY
Retrocopy GLARISLKKEPLYVGADDDKANATVDGLEQGYVVCPSEK*FLLLFTFLKKNRKKKLVVFFSSCMSVKYHY

Parental  ELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARGLDIPEVDWIVQYDPPDDPKEYIHR
          EL.N..DLPVLAIHGKQK.NKRTTTFFQFCNADSGTL.C.DV.ARGLDIP..DWIV.YD..DD.KEYIHR
Retrocopy ELPNCNDLPVLAIHGKQKHNKRTTTFFQFCNADSGTLSCKDVVARGLDIPQADWIVHYDHLDDLKEYIHR

Parental  VGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKNYFLHKSAQEA
          VGRTARGLNGR.H.L.IL.PE...F..YLKQSK.PLSEFDFSWSKISDIQSQLEKLIEKNYFL..SAQEA
Retrocopy VGRTARGLNGRRHVLPILGPEDWVFF-YLKQSKIPLSEFDFSWSKISDIQSQLEKLIEKNYFLSTSAQEA

Parental  YKSYIRAYDSHSLKQIFN-VNNLNLPQVALSFGFKVPPFVDLNVNSNEGKQKKRGGGGGFGYQKTKKVEK
          .KSYI..YDSHSLKQIFN..NNLNLPQVAL.FGFK.P.FVDLNVNSNEGK.KKRGG.GGF.YQKTKKVEK
Retrocopy CKSYIPGYDSHSLKQIFN<LNNLNLPQVALPFGFKMPAFVDLNVNSNEGK*KKRGGSGGFDYQKTKKVEK

Parental  SKIFKHISKKSSDSRQFS
          SKIFKHISKKSS.SRQ.S
Retrocopy SKIFKHISKKSSNSRQLS

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_266 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,