RetrogeneDB ID: retro_nleu_1288

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397287.1:15817635..15818314(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSAT1
• Ensembl ID: ENSNLEG00000002989
• Aliases: None
• Description: Phosphoserine aminotransferase [Source:UniProtKB/TrEMBL;Acc:G1QS05]

Sequence

>retro_nleu_1288
TACAAGGTCATTTTTGTGCAAGAAGGTGGGTCTGGCCAGTTCAGTGCTGTCCCCTTAAACCCAAAGTGCCTGAAAGGAGG
AAGGTGTGCCAACTATGTGGTGACAGGAGCTTGGTCAGCTAAAGCGGCAGAAGCATCCAAGAAGTTTGAGATTGTGAATA
TCAGCTACCCTAAACTTGGGAGTTATATGAAAATTCCAGATTCAACACCTGGAACCTCACCCTTACAGCTTCTATGTGTA
ATGCTGCACAAATGACTGGCACAGAGTGGCGTTTGACTTTATATCTGATCTCAGGAAGCACTACTGGTTTGCCACATATT
CTCAAACTTTCTATCGAAGGCAGTGGATGCTTCCAGGTTTGGTGTGATTTTTGCTGGTGCCCAGAAGCACGTTGGTTGTT
TTGGGATGACAGTAGTGATCATCTGCAATGACTGCTGGGGTTACCCTCAGAGAATGGCCCTCCATCCTGGAATACAAAGT
GCATGTTGGAAACAACTTCTTGTACAACATGCGACAGTATTTCAGCAACTATGTCATGGGCTTGTTACTGGTGTAGATTA
AGAATGATGGCACTGCAGCAGTGACGGAGAAGCTTAGCTCCATCAAATCTAAAATAATAATTTATGATATTTTTACTAAT
TCTTAAGGATTCTATGAACGTCCAGTAGAGCCTCATAAT

Alignment

ORF - retro_nleu_1288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.68 %
• Parental protein coverage: 54.94 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YKVIFLQGGGSGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDP-S
          YKVIF.Q.GGSGQFSAVPLN...LK.GRCA.YVVTGAWSAKAAE..KKF...NI..PKLGSY.KIPD...
Retrocopy YKVIFVQEGGSGQFSAVPLNPKCLKGGRCANYVVTGAWSAKAAEASKKFEIVNISYPKLGSYMKIPDS<N

Parental  TWNL-NPDASYVYYCANETVHGVEFDFIPDVK-GAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAG
          TWNL..P...YV..C.N...H.V.FDFI.D....A.LVC...SNFLSK.VD.S.FGVIFAGAQK.VG..G
Retrocopy TWNL<HPYSFYV*CCTNDW-HRVAFDFISDLR<EALLVCHIFSNFLSKAVDASRFGVIFAGAQKHVGCFG

Parental  VTVVIVRDD-LLGFALQECP-SVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIK
          .TVVI...D.LLG......P.S.LEYKV..GN..LYN....FS.YVMGL.L..IKN.G.AA..EKLSSIK
Retrocopy MTVVIICND<LLGLPSENGP<SILEYKVHVGNNFLYNMRQYFSNYVMGLLLV*IKNDGTAAVTEKLSSIK

Parental  SQ-TIYEIIDNSQGFYVCPVEPQN
          S...IY.I..NS.GFY..PVEP.N
Retrocopy SKIIIYDIFTNS*GFYERPVEPHN

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_1288 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 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006898	1 retrocopy	retro_amel_375,
Bos taurus	ENSBTAG00000013960	1 retrocopy	retro_btau_1658,
Canis familiaris	ENSCAFG00000001570	1 retrocopy	retro_cfam_269,
Choloepus hoffmanni	ENSCHOG00000003817	1 retrocopy	retro_chof_2702,
Callithrix jacchus	ENSCJAG00000003319	1 retrocopy	retro_cjac_1203,
Echinops telfairi	ENSETEG00000004158	1 retrocopy	retro_etel_99,
Homo sapiens	ENSG00000135069	3 retrocopies	retro_hsap_2267, retro_hsap_4054, retro_hsap_412,
Loxodonta africana	ENSLAFG00000017917	2 retrocopies	retro_lafr_1249, retro_lafr_660,
Macaca mulatta	ENSMMUG00000011868	2 retrocopies	retro_mmul_1029, retro_mmul_2341,
Mustela putorius furo	ENSMPUG00000012566	1 retrocopy	retro_mputfur_808,
Nomascus leucogenys	ENSNLEG00000002989	3 retrocopies	retro_nleu_1010, retro_nleu_1288 , retro_nleu_2805,
Oryctolagus cuniculus	ENSOCUG00000007765	1 retrocopy	retro_ocun_1092,
Pongo abelii	ENSPPYG00000019313	3 retrocopies	retro_pabe_1950, retro_pabe_308, retro_pabe_3328,
Pan troglodytes	ENSPTRG00000021045	2 retrocopies	retro_ptro_1606, retro_ptro_316,
Rattus norvegicus	ENSRNOG00000013971	1 retrocopy	retro_rnor_1663,
Tupaia belangeri	ENSTBEG00000012946	1 retrocopy	retro_tbel_1577,
Tarsius syrichta	ENSTSYG00000000093	2 retrocopies	retro_tsyr_1073, retro_tsyr_1212,