RetrogeneDB ID: retro_nleu_2218

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397335.1:8958364..8959540(+)
• Located in intron of: ENSNLEG00000016826

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3D
• Ensembl ID: ENSNLEG00000015502
• Aliases: None
• Description: None

Sequence

>retro_nleu_2218
ATGTCGGAAGGAAATGTGGTGAGCAAACCCAGCACTCTGCAAGGGCCCCAACCCCTCTAACTGGGGCCCAGGAGCTCAAC
AGGCAGCGACTGGCACCCCTTCACCCCGGGCCGCCTTCCCTTCATCCACTCTGGGAACCTTACCCTGGGGGTTGAGGTTG
GGGGTCAAGAAGAAAACCTTCACCCCAAATATCATCAGTCAGAAGAACTCAAGGAAGAAGTAACCATCAAGAAGGAGAAA
CATGAAAGGGACAGAGATGGACAGAGAGAGGTGCATGGACAGGGATGAGGCCACCCAGAAGTGATCCAGTCCCACTCCAT
CTTTGAGAAGGGCCCAGCTGAAATGATGAAGAAAAGAGGAACTGGAATAAGAAAGTGAATGTGTCAGACATGGGACCTTC
TCATATCATCAACATCAAAAAAGAGAAGAAAGAGTTGGACGAACACATGAAACATCTCACCATGCTGGAGAAGGACGATT
TCATCGATGACCCTGGGCTAAGGAATGACACTCGAAACATGCCTGTGCAGCTGCCACTGGCTCACTCATGGTGGCTTTTT
AAGGAAGAAAATGATGAACCAGATGTTAAACCTTGGCTGGCTGGCCCCAAGGAAGAGGTGGATGTACCTACTGTGAAACT
GAAAGAGGAGCTACAAGATGAGGAGGAGGAGGCCAAGTTGAAGGCTCCTTCCAGAGCAGCCAGGAAGACCCCCGGGGCCT
CCCGAAGGACATACCCGTGGCAGAGCTGCCCAGGAGCTGAGCCTCACCAAGGAGGAGGAATTGCTGTTCCTCCAGTTGCC
AGACACCCTCCCTGGCCACCCACCTACCCAGGACATGAAGCCCATCAAGGCAGAGGTACAGGGCAAGGACGGACAGGTGG
TACTCATCAAGCAGGAGAACGACCAGGAAGCCAGGCTGGCAGAGAATGCTTCTACCCTAGCTGACCTGACAGAGGGTCAA
GTTGGCAAGCTGCCCATCTGCAAGTCTGAAAGGTTGCAACTCCTCCTGGGCAAGGTGACTCTGGTCGTGACCATGGGAAC
CGCCTGCTCTTTCCTGCAGGAGCTGGTGTCTGTGGGCCTTGGAGAGAGTAGGACCAGGGAGATGATAGACCTGGGACATA
TGAAGCACAAACTTCTGTGTTCCCCCGATTTTGAATCCCTCTTGGATCACAAACAC

Alignment

ORF - retro_nleu_2218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.39 %
• Parental protein coverage: 99.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSEGNAAGEPSTPGGPRPL-LTGARGLIGRRPAPPLTP-GRLPSIRSRDLTLGGVKKKTFTPNIISRKIK
          MSEGN....PST..GP.PL.LTGA..L..R....PL.P.GRLP.I.S..LTL.GV.......N.......
Retrocopy MSEGNVVSKPSTLQGPQPL<LTGAQEL-NRQRLAPLHP>GRLPFIHSGNLTL-GVEVGGQEENLHPKYHQ

Parental  EEPKEEVTVKKEKR-ERDRDRQREGHGRGRGRPEVIQSHSIFEQGPAEMMKKKG-NWDKTVDVSDMGPSH
          .E...E....K....ERDRD.QRE.HG.G.G.PEVIQSHSIFE.GPAEMMKK.G.NW.K.V.VSDMGPSH
Retrocopy SEELKEEVTIKKEKHERDRDGQREVHGQG*GHPEVIQSHSIFEKGPAEMMKKRG<NWNKKVNVSDMGPSH

Parental  IINIKKEKRETDEETKQILRMLEKDDFLDDPGLRNDTRNMPVQLPLAHSGWLFKEENDEPDIKPWLAGPK
          IINIKKEK.E.DE..K..L.MLEKDDF.DDPGLRNDTRNMPVQLPLAHS.WLFKEENDEPD.KPWLAGPK
Retrocopy IINIKKEKKELDEHMKH-LTMLEKDDFIDDPGLRNDTRNMPVQLPLAHSWWLFKEENDEPDVKPWLAGPK

Parental  EEDMEVDIPAVKVKEEPRDEEEEAKMKAPPKAARKTPGL-PKDVSVAELLRELSLTKEEELLFLQLPDTL
          EE...VD.P.VK.KEE..DEEEEAK.KAP..AARKTPG..P..........ELSLTKEEELLFLQLPDTL
Retrocopy EE---VDVPTVKLKEELQDEEEEAKLKAPSRAARKTPGA>PEGHTRGRAAQELSLTKEEELLFLQLPDTL

Parental  PGQPPTQEIKPIKTEVQGEDGQMVLIKQEKDREAKLAENACTLADLTEGQVGKLLIRKSGRVQLLLGKVT
          PG.PPTQ..KPIK.EVQG.DGQ.VLIKQE.D.EA.LAENA.TLADLTEGQVGKL.I.KS.R.QLLLGKVT
Retrocopy PGHPPTQDMKPIKAEVQGKDGQVVLIKQENDQEARLAENASTLADLTEGQVGKLPICKSERLQLLLGKVT

Parental  LDVTMGTACSFLQELVSVSLGDSRTGEMTVLGHVKHKLVCSPDFESLLDHKH
          L.VTMGTACSFLQELVSV.LG.SRT.EM..LGH.KHKL.CSPDFESLLDHKH
Retrocopy LVVTMGTACSFLQELVSVGLGESRTREMIDLGHMKHKLLCSPDFESLLDHKH

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_2218 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013488	1 retrocopy	retro_dnov_1681,
Equus caballus	ENSECAG00000025090	1 retrocopy	retro_ecab_43,
Erinaceus europaeus	ENSEEUG00000007632	2 retrocopies	retro_eeur_277, retro_eeur_705,
Homo sapiens	ENSG00000168495	1 retrocopy	retro_hsap_596,
Macropus eugenii	ENSMEUG00000000465	1 retrocopy	retro_meug_1550,
Myotis lucifugus	ENSMLUG00000002109	1 retrocopy	retro_mluc_2339,
Macaca mulatta	ENSMMUG00000023226	1 retrocopy	retro_mmul_2449,
Monodelphis domestica	ENSMODG00000009491	1 retrocopy	retro_mdom_988,
Nomascus leucogenys	ENSNLEG00000015502	1 retrocopy	retro_nleu_2218 ,
Pongo abelii	ENSPPYG00000018419	1 retrocopy	retro_pabe_594,
Pan troglodytes	ENSPTRG00000020056	1 retrocopy	retro_ptro_439,
Tursiops truncatus	ENSTTRG00000012745	1 retrocopy	retro_ttru_1189,