RetrogeneDB ID: retro_nleu_590

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397268.1:14519554..14520949(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000004625
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AP5M1
• Ensembl ID: ENSNLEG00000013007
• Aliases: None
• Description: None

Sequence

>retro_nleu_590
CGGTATCCAACTGTTGAAAAACGAGCCAGAGTCTTCAGTGGAGCAAGTTATGTGCCTGTTCCCGAAGATGGTCCCTTTCT
TAAAGCACTGCTCTTTGAACTTAGATTATTGGATGATGATAAAGACTTTGTTGAGAGTCGTGATAGCTGTTCACGCATCA
ATAAAACATCCATTTATGGAATCCTGATAGGAGGTGAAGAACTCTGGCCAGTTGTTGCTTTTCTGAAGAATGACATGATA
TATGCCTGTGTTCCACTAGTTGAACAAAGTCTGTCACCTTGACCACCATTAATTAGTGTTAGTGGAGTTTCACAAGGCTT
TGAATTTCTTTTTGGGTTACAGGATTTTCTTTATTCAGGTCAAAAAAATGACTCTGAGCTACATACAAAATTGAGCCAGT
TGCCTGACTTGCTTCTGCAAGCTTGTCCATTTGGTACTTTACTAGATGCCAACTTACAGAATTCATTAGATAATACCAAC
TTTGCATCTGTGACTCAGCCACAAAAACAGCCAGCTTGGAAAACTGGAACGTACAAAGGAAAACCACAAGTTTCTATTTC
TATCACTGAAAAGGTAAAATCCATGCAATATGATAAACAGGGTGTCGCGGATACATGGCAAGTTGTTGGAACAGTGACTT
GCAAGTGTGATTTGGAAGGAATCATGCCAAATGTTACCATCAGCTTGAGTCTCCCCACCAATGGATCTCCACTTCAGGAT
ATTCTAGTTCATCCTTGTGTAACTTCTCTTGACTCTGCAATTCTGACTTCTAGTAGTATTGATGCAATGGATGACTCTGC
ATTTAGTGGGCCTTACAAATTTCCATTCACTCTACCTTTAGAGTCATTCAGCTTATGCTACTACACTTCCCAGGTCCCTG
TCCCACCAATTTTGGGTTTTTATCAAATGAAGGAGGAAGAAGTACAACTAAGAATAACCATTAATTTAAAACTTCATGAA
AGTGTGAAAAATAATTTTGAATTCTGTGAAGCCCATATACCTTTTTACAATAGAGGTCCAATTACACATTTGGAATACAA
AACTAGTTTTGGCCAGCTCGAAGTATTTCGAGAGAAAAGCTTATTGATCTGGATTATTGGCCAGAAGTTCCCAAAATCAA
TGGAAATTAGTCTTTCTGGAACTGTAACTTTTGGAGCCAAGAGCCATGAGAAGCAGCAATTTGACCCAATTTGTATTGGA
CAAACAGCATATTTAAAGCTTCATTTTAGGATCTTAGATTACACACTTACTGGATGTTATGCAGATCAGCATTCAGTTCA
AGTTTTTGCATCAGGAAAACCAAAAATAAGTGCACACCGGAAACTAATTTCTTCTGATTATTACATCTGGAATTCGAAAG
CCCCTGCTCCAGTAACATATGGATCATTATTATTG

Alignment

ORF - retro_nleu_590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.85 %
• Parental protein coverage: 92.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYPTVEKRARVFNGASYVPVPEDGPFLKALLFELRLLDDDKDFVESRDSCSRINKTSVYGLLIGGEELWP
          RYPTVEKRARVF.GASYVPVPEDGPFLKALLFELRLLDDDKDFVESRDSCSRINKTS.YG.LIGGEELWP
Retrocopy RYPTVEKRARVFSGASYVPVPEDGPFLKALLFELRLLDDDKDFVESRDSCSRINKTSIYGILIGGEELWP

Parental  VVAFLKNDMIYACVPLVEQTLSPRPPLISVSGVSQGFEFLFGIQDFLYSGQKNDSELNTKLSQLPDLLLQ
          VVAFLKNDMIYACVPLVEQ.LSP.PPLISVSGVSQGFEFLFG.QDFLYSGQKNDSEL.TKLSQLPDLLLQ
Retrocopy VVAFLKNDMIYACVPLVEQSLSP*PPLISVSGVSQGFEFLFGLQDFLYSGQKNDSELHTKLSQLPDLLLQ

Parental  ACPFGTLLDANLQNSLDNTNFASVTQPQKQPAWKTGTYKGKPQVSISITEKVKSMQYDKQGVADTWQVVG
          ACPFGTLLDANLQNSLDNTNFASVTQPQKQPAWKTGTYKGKPQVSISITEKVKSMQYDKQGVADTWQVVG
Retrocopy ACPFGTLLDANLQNSLDNTNFASVTQPQKQPAWKTGTYKGKPQVSISITEKVKSMQYDKQGVADTWQVVG

Parental  TVTCKCDLEGIMPNVTISLSLPTNGSPLQDILVHPCVTSLDSAILTSSSIDAMDDSAFSGPYKFPFTPPL
          TVTCKCDLEGIMPNVTISLSLPTNGSPLQDILVHPCVTSLDSAILTSSSIDAMDDSAFSGPYKFPFT.PL
Retrocopy TVTCKCDLEGIMPNVTISLSLPTNGSPLQDILVHPCVTSLDSAILTSSSIDAMDDSAFSGPYKFPFTLPL

Parental  ESFNLCYYTSQVPVPPILGFYQMKEEEVQLRITINLKLHESVKNNFEFCEAHIPFYNRGPITHLEYKTSF
          ESF.LCYYTSQVPVPPILGFYQMKEEEVQLRITINLKLHESVKNNFEFCEAHIPFYNRGPITHLEYKTSF
Retrocopy ESFSLCYYTSQVPVPPILGFYQMKEEEVQLRITINLKLHESVKNNFEFCEAHIPFYNRGPITHLEYKTSF

Parental  GQLEVFREKSLLIWIIGQKFPKSMEISLSGTVTFGAKSHEKQPFDPICIGQTAYLKLHFRILDYTLTGCY
          GQLEVFREKSLLIWIIGQKFPKSMEISLSGTVTFGAKSHEKQ.FDPICIGQTAYLKLHFRILDYTLTGCY
Retrocopy GQLEVFREKSLLIWIIGQKFPKSMEISLSGTVTFGAKSHEKQQFDPICIGQTAYLKLHFRILDYTLTGCY

Parental  ADQHSVQVFASGKPKISAHRKLISSDYYIWNSKAPAPVTYGSLLL
          ADQHSVQVFASGKPKISAHRKLISSDYYIWNSKAPAPVTYGSLLL
Retrocopy ADQHSVQVFASGKPKISAHRKLISSDYYIWNSKAPAPVTYGSLLL

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_590 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002388	1 retrocopy	retro_amel_1700,
Canis familiaris	ENSCAFG00000015249	1 retrocopy	retro_cfam_1676,
Mustela putorius furo	ENSMPUG00000005943	1 retrocopy	retro_mputfur_210,
Nomascus leucogenys	ENSNLEG00000013007	1 retrocopy	retro_nleu_590 ,
Ictidomys tridecemlineatus	ENSSTOG00000011073	1 retrocopy	retro_itri_993,
Tupaia belangeri	ENSTBEG00000010976	1 retrocopy	retro_tbel_167,