RetrogeneDB ID: retro_nleu_431

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397265.1:3396717..3397628(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPAT
• Ensembl ID: ENSNLEG00000008762
• Aliases: None
• Description: Amidophosphoribosyltransferase [Source:UniProtKB/TrEMBL;Acc:G1RBV9]

Sequence

>retro_nleu_431
CTGCAGCGCCGGGGTCAGGAGAGTGCTGGTATCGTGACTAGTGACGGGAGTTCAGTGCCAACATTCAAATCACACAAGGG
AATGGGTCTTGTAAATCACGTCTTTACTGAAGACAGTTTGAAAAAATTATATGTTTCAAATCTTGGAATGGGACACACAA
GGTATGCCACCACAGGAAAATGTGAATTAGAAAATTGTCAGCCCTTTGTTGTTGAAACACTTCATGGGAAGATAGCTGTG
GCACATAATGGCGAATTGGTGAATGCTGCTCGACTAAGGAAAAAGCTTCTGCGTCATGGTATTGGTCTGTCCACAAGTTC
TGATAGTGAAGTGATTACCCAGTTAGTGGCGTATACCCCTCCTCAGGAACAAGATGACACCCCAGACTGGGTAGCCAGGA
TTAAAAACTTGATGAAGGAAGCACCCACAGCATACTCCCTGCTTGTAATGCACAGAGATGTTATTTATGCAGTACAAGAT
CCTTATGGAAATCATCCCTTATGCATTGATCGTCTTATTCCAGTGTCTGATATAAATGACAAAGAGAAAAAAACACCAGA
AACAGAAGGATGGGTGGTGTCTTCAGAATCTTGTAGCTTCTTGTCTATTGGTGCAAGATATTATCGAGAATTCTTGCCTG
CAGAATTTATGGAAATATTCAGACATAATGTCCGAACTCTTGATATTATATCAAGGTCTGAGCGAACCCTATGGCTTTTT
GTATCTTTGAATATGTTTATTTTGCAAGACCAGACAGTACGTTTGAAGACCAAATGGTTTATACAGTAAGATACCGTTGT
GGCCAGCAGCTAGCGATTGAAGCACCTGTGGATGCAGATTTGGTTAGCACTGTTCCAGAATCTGCTACGCCTGCTGCTCT
TGCGTATGCAGGAAAGTGTGGACTTGAATTC

Alignment

ORF - retro_nleu_431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.11 %
• Parental protein coverage: 58.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQHRGQESAGIVTSDGSSVPTFKSHKGMGLVNHVFTEDNLKKLYVSNLGIGHTRYATTGKCELENCQPFV
          LQ.RGQESAGIVTSDGSSVPTFKSHKGMGLVNHVFTED.LKKLYVSNLG.GHTRYATTGKCELENCQPFV
Retrocopy LQRRGQESAGIVTSDGSSVPTFKSHKGMGLVNHVFTEDSLKKLYVSNLGMGHTRYATTGKCELENCQPFV

Parental  VETLHGKIAVAHNGELVNAARLRKKLLRHGIGLSTSSDSEMITQLLAYTPPQEQDDTPDWVARIKNLMKE
          VETLHGKIAVAHNGELVNAARLRKKLLRHGIGLSTSSDSE.ITQL.AYTPPQEQDDTPDWVARIKNLMKE
Retrocopy VETLHGKIAVAHNGELVNAARLRKKLLRHGIGLSTSSDSEVITQLVAYTPPQEQDDTPDWVARIKNLMKE

Parental  APTAYSLLIMHRDVIYAVRDPYGNRPLCIGRLIPVSDINDKEKKTSETEGWVVSSESCSFLSIGARYYRE
          APTAYSLL.MHRDVIYAV.DPYGN.PLCI.RLIPVSDINDKEKKT.ETEGWVVSSESCSFLSIGARYYRE
Retrocopy APTAYSLLVMHRDVIYAVQDPYGNHPLCIDRLIPVSDINDKEKKTPETEGWVVSSESCSFLSIGARYYRE

Parental  VLPGEIVEISRHNVRTLDIISRSE-GNSMAFCIFEYVYFARPDSMFEDQMVYTVRYRCGQQLAIEAPVDA
          .LP.E..EI.RHNVRTLDIISRSE..N.MAFCIFEYVYFARPDS.FEDQMVYTVRYRCGQQLAIEAPVDA
Retrocopy FLPAEFMEIFRHNVRTLDIISRSE<ANPMAFCIFEYVYFARPDSTFEDQMVYTVRYRCGQQLAIEAPVDA

Parental  DLVSTVPESATPAALAYAGKCGLPY
          DLVSTVPESATPAALAYAGKCGL..
Retrocopy DLVSTVPESATPAALAYAGKCGLEF

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_431 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023644	2 retrocopies	retro_ecab_1113, retro_ecab_270,
Homo sapiens	ENSG00000128059	1 retrocopy	retro_hsap_2809,
Gorilla gorilla	ENSGGOG00000004608	1 retrocopy	retro_ggor_1953,
Monodelphis domestica	ENSMODG00000020693	1 retrocopy	retro_mdom_1487,
Nomascus leucogenys	ENSNLEG00000008762	1 retrocopy	retro_nleu_431 ,
Pongo abelii	ENSPPYG00000029568	1 retrocopy	retro_pabe_2306,
Pan troglodytes	ENSPTRG00000016080	1 retrocopy	retro_ptro_1903,
Tursiops truncatus	ENSTTRG00000010928	1 retrocopy	retro_ttru_794,