RetrogeneDB ID: retro_nleu_1359

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397290.1:19365233..19366375(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP50
• Ensembl ID: ENSNLEG00000013154
• Aliases: None
• Description: None

Sequence

>retro_nleu_1359
AGAGCCATAAAGAAAGCAAAGCGCAGAAATGTTGGATTCGAATCTGACAGTGGAGGAGCCTTTCAAGGTTTTAAAGGTTT
AGTGGTACCTTCTGGAGGAGGATGGTTTCCTGGATTTGGTAGTGGTGCTGGAGGGAAGCCTTTCGAAGGACTGTCGAATG
GAAACAACATAACCAGCGCCCCTCCCTTCACCAGTGCAAAAGCAGTGGCAGAGCCCAAGGTAGCCTTTGGTTCTCTTGCT
GCAAATGGCCCTGCCGCCTTGGTTGGTAAAAAAGTTTCAAATCCCCAAACTAATGGGGACAGTCAGCAGCCCTCCTCCTC
TGGCCTTCCTTCCAGTAAAGCTTGTGTCGGAAATGCCTATTAGAAGCAGTTGGCCGCCTTGAACTGCTCCGTGCGGGATT
GGATAGTGAAGCATGTGAATACAAAGCCCCTCTGTGATCTGACACCTATCTTTAAAGACTATGAGAAATATTTAGCAAAC
ATTGAACAGCAACACGAGAACAGTGGCAGGAATTCTGAAAGTGAATCTAACAAAGCTGCGGCTGAAACACAGTCTCCTTC
CCTTTTTGGCTCAACAAAATTACAGCAAGAGTCAGCGTTTTTGTTTCATGGCAACAAAACTGAAGATGCACCTGACAAGA
AGGTGGAGGTGGCATCTGAAAAGAAAACGGACCCATCATCACTAGGAGCGACAAGTGCCTCATTTAATTTTGGCAAGAAA
GTTGATAGCTCTGTTTTGGGCTCATTAAGCTCTGTCCCCCTGACTGGATTTTCATTCTCCCCTGGAAACTCCAGTTTATT
TGGCAAAGATATTACCCAGAGTAAACCAGTCTCTTCACCATTTGCCACTAAACCATTGGAGGGCCGAGCAGAAGGTGACA
GTGGTGAATGCAAAGGTGGAGATGAAGAAGAGAATGATGAGCCACCCAAAGTAGTAGTTACCGAAGTAAAAGAAGAAGAT
GCTTTTTATTCCAAAAAGTGTAAACTATTTTACAAGAAAGATAATGAGTTTAAAGAGAAAGGCATAGGTACTCTGCATTT
AAAACTACAGCAAATCAGAAGACACAGCTTTTGGTGCGGGCAGACACCAATTTAGGCAACAGATTGCTGAATGTTCTGAT
TCCACCCAATATGCCATGTACG

Alignment

ORF - retro_nleu_1359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.03 %
• Parental protein coverage: 81.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RAIKKAKRRNVGFESDSGGAFKGFKGLVVPSGGGRFPGFGSGAGGKPLEGLSNGNNITSALPFTSAKAVA
          RAIKKAKRRNVGFESDSGGAF.GFKGLVVPSGGG.FPGFGSGAGGKP.EGLSNGNNITSA.PFTSAKAVA
Retrocopy RAIKKAKRRNVGFESDSGGAFQGFKGLVVPSGGGWFPGFGSGAGGKPFEGLSNGNNITSAPPFTSAKAVA

Parental  EPKVAFGSLAANGPTTLVDKKVSNPKTNGDSQQPSSSGLASSKACVGNAYHKQLAALNCSVRDWIVKHVN
          EPKVAFGSLAANGP..LV.KKVSNP.TNGDSQQPSSSGL.SSKACVGNAY.KQLAALNCSVRDWIVKHVN
Retrocopy EPKVAFGSLAANGPAALVGKKVSNPQTNGDSQQPSSSGLPSSKACVGNAY*KQLAALNCSVRDWIVKHVN

Parental  TNPLCDLTPIFKDYEKYLANIEQQHGNSGRNSESESNKAAAETQSPSLFGSTKLQQESTFLFHGNKTEDT
          T.PLCDLTPIFKDYEKYLANIEQQH.NSGRNSESESNKAAAETQSPSLFGSTKLQQES.FLFHGNKTED.
Retrocopy TKPLCDLTPIFKDYEKYLANIEQQHENSGRNSESESNKAAAETQSPSLFGSTKLQQESAFLFHGNKTEDA

Parental  PDKKVEVASEKKTDPSSLGATSASFNFGKKVDSSVLGSLSSVPLTGFSFSPGNSSLFGKDITQSKPVSSP
          PDKKVEVASEKKTDPSSLGATSASFNFGKKVDSSVLGSLSSVPLTGFSFSPGNSSLFGKDITQSKPVSSP
Retrocopy PDKKVEVASEKKTDPSSLGATSASFNFGKKVDSSVLGSLSSVPLTGFSFSPGNSSLFGKDITQSKPVSSP

Parental  FPTKPLEGQAEGDSGECKGGDEEENDEPPKVVVTEVKEEDAFYSKKCKLFYKKDNEFKEKGIGTLHL-KP
          F.TKPLEG.AEGDSGECKGGDEEENDEPPKVVVTEVKEEDAFYSKKCKLFYKKDNEFKEKGIGTLHL.K.
Retrocopy FATKPLEGRAEGDSGECKGGDEEENDEPPKVVVTEVKEEDAFYSKKCKLFYKKDNEFKEKGIGTLHL<KT

Parental  TANQKTQLLVRADTNLGNILLNVLIPPNMPCT
          TANQKTQLLVRADTNLGN.LLNVLIPPNMPCT
Retrocopy TANQKTQLLVRADTNLGNRLLNVLIPPNMPCT

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_1359 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016242	1 retrocopy	retro_cjac_4080,
Homo sapiens	ENSG00000093000	3 retrocopies	retro_hsap_1429, retro_hsap_3301, retro_hsap_3434,
Microcebus murinus	ENSMICG00000006840	1 retrocopy	retro_mmur_534,
Mus musculus	ENSMUSG00000016619	1 retrocopy	retro_mmus_1905,
Nomascus leucogenys	ENSNLEG00000013154	2 retrocopies	retro_nleu_1359 , retro_nleu_1844,
Otolemur garnettii	ENSOGAG00000002320	1 retrocopy	retro_ogar_942,
Pongo abelii	ENSPPYG00000011928	1 retrocopy	retro_pabe_2723,