RetrogeneDB ID: retro_nleu_1844

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397312.1:15570184..15571571(-)
• 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_1844
CGAGAAGGAACTGACAGGAATTGGGATCAAGAAGATGAAGCTGAAGAGATGGGAACATTCTCCGTGGCCAGTGAGGAAGT
CTTGAAGAATAGAGCCATAAAGAAAGCAAAGCGCAGAAATGTTGGATTCGAATCTGACAGTGGAGGAGACTTTAAAGATT
TTAAAGGTTTGGTGGTACCTTCTGGAGGAGGACGGTTTCCTGGATTTGGTAGTGGCGCTGGAGGGGAAGCCTTTGGAAGG
ACTGTCGAATGGAAACAACATAACCAGTGCCCCTCCCTTCACCGGTGCAAAGGCAGTGGCAGAGCCCAAGGTAGCCTTTG
GTTCTCTTGCTGCAAATGGCCCTACCGCCTTGGTCGATAAAAAAGTTTCAAATCCCAAAACTAATGGGGACTGTCAGCAG
CCCTCCTCCTCTGGCCTTGCTTCCAGTAAAGCTTGTGTCGGAAATGCCTGTCACAAGCAGTTGGCCGCCTTGAACTGCTC
TGTGCGGGATTGGATAGTGAAGCACGTGAATACAAATCCCCTCTGTGATCTGACACCTATCTTTAAAGACTATGAGAAAT
ATTTAGCAAACATTGAACAGCAACATGGGAACAATGGCAGGAATTCTGAAAGTGAATCTAACAAAGCGGCGGCTGAAACA
CAGTCTCCTTCCCTTTTTGGCTCAACAAAATTACAGCAAGAGTCAACGTTTCTGTTTCATGGCAACAAAACTGAAGATAA
CACCTGACAAGAAGGTGGAGGTGGCATCTGAAAAGAAAACGGACCCATCATCACTAGGAGCGACAAGTGCCTCATTTAAT
TTTGGCAAGAAAGTTGATAGCTCTGTTTTGGGCTCATTAAGCTCTGTCCCCCTGACTGGATTTTCATTCTCCCCTGGAAA
CTCCAATTTATTTGGCAAAGATATTACCCAGAGTAAACCAGTCTCTTCACCATTTCCCACTAAACCATTTGAGGCCAAGC
GGAAGGTGACAGTGGTGAATGCAAAGGTGGAGATTAAGAAAAGAATGATGAGCCACCCAAAGTAGTAGTTACAGAAGTAA
AAGAAGAAGATGCTTTTTACTCCAAAAAGTGTAAACTATTTTACAAGAAAGACAATGAGTTTAAAGAGAAAGGCATAGGT
ACTCTGCATTTAAAACCTACAGCAAATCAGAAGACACAGCTTTTGGTGCGGGCAGACACCAATTTAGGCAACATATTGCT
GAATGTTCTGATTCCACCCAATATGCCATGTACGCGAACAGGGAAAAATAACGTGCTTATCGTCTGTGTTCCAAATCCAC
CAATCGACGAGAAGAATGCCACCATTCCAGTCACCATGTTGATTCGGGTAGAAACCAGCGAGGATGCAGACGAGTTGCAC
AAAATTTTACTGGAGAAAAAGGATGCC

Alignment

ORF - retro_nleu_1844 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.7 %
• Parental protein coverage: 98.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KELTDRNWDQEDEAEEVGTFSVASEEVLKNRAIKKAKRRNVGFESDSGGAFKGFKGLVVPSGGGRFPGFG
          .E.TDRNWDQEDEAEE.GTFSVASEEVLKNRAIKKAKRRNVGFESDSGG.FK.FKGLVVPSGGGRFPGFG
Retrocopy REGTDRNWDQEDEAEEMGTFSVASEEVLKNRAIKKAKRRNVGFESDSGGDFKDFKGLVVPSGGGRFPGFG

Parental  SGAGG-KPLEGLSNGNNITSALPFTSAKAVAEPKVAFGSLAANGPTTLVDKKVSNPKTNGDSQQPSSSGL
          SGAGG.KPLEGLSNGNNITSA.PFT.AKAVAEPKVAFGSLAANGPT.LVDKKVSNPKTNGD.QQPSSSGL
Retrocopy SGAGG>KPLEGLSNGNNITSAPPFTGAKAVAEPKVAFGSLAANGPTALVDKKVSNPKTNGDCQQPSSSGL

Parental  ASSKACVGNAYHKQLAALNCSVRDWIVKHVNTNPLCDLTPIFKDYEKYLANIEQQHGNSGRNSESESNKA
          ASSKACVGNA.HKQLAALNCSVRDWIVKHVNTNPLCDLTPIFKDYEKYLANIEQQHGN.GRNSESESNKA
Retrocopy ASSKACVGNACHKQLAALNCSVRDWIVKHVNTNPLCDLTPIFKDYEKYLANIEQQHGNNGRNSESESNKA

Parental  AAETQSPSLFGSTKLQQESTFLFHGNKTED-TPDKKVEVASEKKTDPSSLGATSASFNFGKKVDSSVLGS
          AAETQSPSLFGSTKLQQESTFLFHGNKTED.TPDKKVEVASEKKTDPSSLGATSASFNFGKKVDSSVLGS
Retrocopy AAETQSPSLFGSTKLQQESTFLFHGNKTED>TPDKKVEVASEKKTDPSSLGATSASFNFGKKVDSSVLGS

Parental  LSSVPLTGFSFSPGNSSLFGKDITQSKPVSSPFPTKPLE-GQAEGDSGECKGGDEEENDEPPKVVVTEVK
          LSSVPLTGFSFSPGNS.LFGKDITQSKPVSSPFPTKP.E.GQAEGDSGECKGGD.E.NDEPPKVVVTEVK
Retrocopy LSSVPLTGFSFSPGNSNLFGKDITQSKPVSSPFPTKPFE<GQAEGDSGECKGGD*EKNDEPPKVVVTEVK

Parental  EEDAFYSKKCKLFYKKDNEFKEKGIGTLHLKPTANQKTQLLVRADTNLGNILLNVLIPPNMPCTRTGKNN
          EEDAFYSKKCKLFYKKDNEFKEKGIGTLHLKPTANQKTQLLVRADTNLGNILLNVLIPPNMPCTRTGKNN
Retrocopy EEDAFYSKKCKLFYKKDNEFKEKGIGTLHLKPTANQKTQLLVRADTNLGNILLNVLIPPNMPCTRTGKNN

Parental  VLIVCVPNPPIDEKNATMPVTMLIRVKTSEDADELHKILLEKKDA
          VLIVCVPNPPIDEKNAT.PVTMLIRV.TSEDADELHKILLEKKDA
Retrocopy VLIVCVPNPPIDEKNATIPVTMLIRVETSEDADELHKILLEKKDA

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_1844 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,