RetrogeneDB ID: retro_nleu_2805

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397435.1:2504505..2505696(-)
• 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_2805
CTCGCACCGCAGACGCCAGGAACGCTCGCAGTTCACATGCTCAGTCCTCCCTGGCTGACTCACCACCCATGCTGCCGCAG
CATGGACGCCCCGGGGTATGTGGTCAACTTTGGGCCTGGTCCAGCCAAGCTGCCACACTCAGGGTTGTTAGAGATACAAA
AGGAATTATTAGACTACAAAGGAATTGGCATTAGTATTCTTGAAATGAGTCACAGGTCGTCAAATTTTATCAAGATGATT
AACAATGCAGAGAATCTTGTGCGGGAATTGCTAGCTGTTCCAGACAACTACGAGGTGATTTTTGTGCAAGGAGGTGGGTC
GAGCCAGTTCAGTGCTGTCCCATTAAAGCTGATTGGCTTGAAAGCAGGAAAGAGTGTGGACTATGTGGTGACAGGAGCTT
GGTCAGCTAAGGCTGTAGAAGAAGCAAAGAAGTTTGGGACTATAAATATTGTTCACTCTAAACTTGGGAGTTATACCTAA
ATTCCAGATCCAAGCACCTGGAGCCTCAACCCGGATGCCTCCTACGTGTATTATTGCGCAAATGGGACGGTGCATGGCGT
GGAGTTTGACTTTATACCCGATGTCAAAAGAGCAGTGCTGGTTTGTGACATGTTCTCAAACTTCCTGTCCAAGCCAGTGG
ATGTTTCCAAGTTTGATGTGATTTTTTCTGGTGCCCAGAAGAATGTTGGCTCTGCTGGGGTCACTGTGGTGATTGTCCGT
GATGACCAACTGAGGTTTGCCCTCCGAGAGTCAACCTCAGTCCTGGAATGCAAGGTGCAGGCTGGAAACAGCTCCTCGTA
CAACACGCCTCCATGTTTCAGCATCTACATCATGGGCTTGGTCCTGGAATGGATTAAAAACAATGGAGGTGCTGCTGCCA
TGGAGAAGCTTAGCTCCATCAAATCCCAAATGATTTATGAGATTACTGATAATTCTCATGGATTCTACATATGTCCAGTG
GAGCCCCAAAATAGAAGCAAGATGAATATTCCATTCTGCATTGGCAATGTCAAAGGAGATGATGCTTTAGTAAAAAGATT
TCTAGATAAAGCTTTTGAACTCAATATGTTGTCCTTGAAAGGGCACAGGTCTGTGGGAGGCATCCAGGCCTCTCTGTACA
ATTCTGTCACAATTGAAGATGTTCAGAAGCTGGCCGCCTTCATGAAAAATTTTTTGGAGATGCGTCAGCTA

Alignment

ORF - retro_nleu_2805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.15 %
• Parental protein coverage: 95.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSPQRPGTPAVHAFGPPWLTHRPRRRTMDAPRQVVNFGPGPAKLPHSVLLEIQKELLDYKGVGISVLEMS
          L.PQ.PGT.AVH...PPWLTH.P..R.MDAP..VVNFGPGPAKLPHS.LLEIQKELLDYKG.GIS.LEMS
Retrocopy LAPQTPGTLAVHMLSPPWLTHHPCCRSMDAPGYVVNFGPGPAKLPHSGLLEIQKELLDYKGIGISILEMS

Parental  HRSSDFAKIINNTENLVRELLAVPDNYKVIFLQGGGSGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAE
          HRSS.F.K.INN.ENLVRELLAVPDNY.VIF.QGGGS.QFSAVPL.LIGLKAG...DYVVTGAWSAKA.E
Retrocopy HRSSNFIKMINNAENLVRELLAVPDNYEVIFVQGGGSSQFSAVPLKLIGLKAGKSVDYVVTGAWSAKAVE

Parental  EAKKFGTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLS
          EAKKFGTINIVH.KLGSYT.IPDPSTW.LNPDASYVYYCAN.TVHGVEFDFIPDVK.AVLVCDM.SNFLS
Retrocopy EAKKFGTINIVHSKLGSYT*IPDPSTWSLNPDASYVYYCANGTVHGVEFDFIPDVKRAVLVCDMFSNFLS

Parental  KPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALQECPSVLEYKVQAGNSSLYNTPPCFSIYVMGL
          KPVDVSKF.VIF.GAQKNVGSAGVTVVIVRDD.L.FAL.E..SVLE.KVQAGNSS.YNTPPCFSIY.MGL
Retrocopy KPVDVSKFDVIFSGAQKNVGSAGVTVVIVRDDQLRFALRESTSVLECKVQAGNSSSYNTPPCFSIYIMGL

Parental  VLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDK
          VLEWIKNNGGAAAMEKLSSIKSQ.IYEI.DNS.GFY.CPVEPQNRSKMNIPF.IGN.KGDDAL.KRFLDK
Retrocopy VLEWIKNNGGAAAMEKLSSIKSQMIYEITDNSHGFYICPVEPQNRSKMNIPFCIGNVKGDDALVKRFLDK

Parental  ALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAAFMKKFLEMHQL
          A.ELNMLSLKGHRSVGGI.ASLYN.VTIEDVQKLAAFMK.FLEM.QL
Retrocopy AFELNMLSLKGHRSVGGIQASLYNSVTIEDVQKLAAFMKNFLEMRQL

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_2805 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,