RetrogeneDB ID: retro_nleu_1010

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397278.1:11870825..11871451(-)
• 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_1010
GGAACGCTATCCGTTCACGTGTTCAGTCCTCCTTGGCTGACTTGCCGCCCTCGCCGCCGTACCGTGGGCATCCCGAGGCA
GGTGGTCAACTTCGGGCCTGGTCCCGCCAAGCTGCCTCACTCAGTGTTAGAGATTAAAAAAAGGAATTATTAGACTACAA
AGGAGTTGGCATTAGTGTTCTTGAAATGAGTCACAGGCCATCAGATGTTGCCAAGATTATTAACAATACAGAGAATCTTG
TGTGGGAATTCCTAGCCGTTCCAGACAACTATAAGGTGATTTTTGTGCAAGGAAGTGGGTCCGGCCAGTTCGGTGCTGTC
CCCTTAAACCTGATTGGCTTGAAAGCAGAAAGACGTGCGGACTATGTGGTGATAGGAGCTTGGTCAGCTAAGGCCGCAGA
AGCAGCCAAGAAGTTTGGGACTATAAATATCATTCACCCTAAACTTAGGAGTTACACAAAAATTCCAGATCCAAGCACCT
GGAACCTCAACCCGGATGCCTCCTACGTGTATCACTGCACAAATGAGATGGTATATGGTGTGGAGTTTGACGTTACACCC
GATGTCAAGGGAGCAGTACTGGTTTGTGACATGTCCTCAAACTTCCTGTCCAAGCCAGTGGATGTC

Alignment

ORF - retro_nleu_1010 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.76 %
• Parental protein coverage: 50.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTPAVHAFGPPWLTHRPRRRTMDAPRQVVNFGPGPAKLPHSVL-LEIQKELLDYKGVGISVLEMSHRSSD
          GT..VH.F.PPWLT.RPRRRT...PRQVVNFGPGPAKLPHSVL.....KELLDYKGVGISVLEMSHR.SD
Retrocopy GTLSVHVFSPPWLTCRPRRRTVGIPRQVVNFGPGPAKLPHSVL<RD*KKELLDYKGVGISVLEMSHRPSD

Parental  FAKIINNTENLVRELLAVPDNYKVIFLQGGGSGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKF
          .AKIINNTENLV.E.LAVPDNYKVIF.QG.GSGQF.AVPLNLIGLKA.R.ADYVV.GAWSAKAAE.AKKF
Retrocopy VAKIINNTENLVWEFLAVPDNYKVIFVQGSGSGQFGAVPLNLIGLKAERRADYVVIGAWSAKAAEAAKKF

Parental  GTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDV
          GTINI.HPKL.SYTKIPDPSTWNLNPDASYVY.C.NE.V.GVEFD..PDVKGAVLVCDMSSNFLSKPVDV
Retrocopy GTINIIHPKLRSYTKIPDPSTWNLNPDASYVYHCTNEMVYGVEFDVTPDVKGAVLVCDMSSNFLSKPVDV

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_1010 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,