RetrogeneDB ID: retro_nleu_2019

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397323.1:7358025..7358947(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP35
• Ensembl ID: ENSNLEG00000006423
• Aliases: None
• Description: None

Sequence

>retro_nleu_2019
GTTGCTGACACAATGGCAGCCTTTGCCATGGAACTCCAGGCACCCGCATTAGGATCTGAACCGATGATGCTGGCTTCATC
TCCAAAGCCAGGAGTTAATGCCCAGTTCTAACCTGGATTTTGAATGCGGAATTTGCCAGCTCTGGTGACTCCTCAGCCTC
AATCAATTAGTGGCCCTTTGATAGGAGTAATGGAAATGAGATCACCTTTACTCGCAGGTGGGTCACCACCACAACCAGTT
GTACTAGCTCAGAAAGATAAAAGTGGCGCTCCACAAGTTAGAAGTATATATGATGACATTTCTAGCCTGGGACTTGGATC
AACACCTTTAACTTCAAGAAGACAGCCAGACATTTCATAATGCAGAGTTCTCTTACTGGAGTTACATCGACTCCTGGAAC
AGGGCAAAGTATGTTTAGTCCAGCAAATATCGGTCAGCCATGAAAGATGACATTATCTCCTTCCCAGTTGGATTCTTTTT
ATACTCAAGGAGATTCTTTGACTTCAGAAGATCACCTTGATGACACTTGGGTGACTGTGTTTGGGTTTTCTCAAGCCTCT
GCTTCCTACATATTATTACAATTTGCACAGTATGGGAATATCTTAAAACACATGATGTCTAACACAGGAAATTGACTGTA
TATTCATTATCAGTCTAAACTGCAGGCTTGGAAAGCCTTAACCAAAGATGGGAGGATTTTTAGAGAATTCATCGTGATTG
GTGTAAAACCCTGTATTGACTAAAGTGTAATGGGAAGCACTGACAGACATGTTTATCATCTCCATCTTTCGCCTTTACAC
CACCAATCAAAACTTTAGGTACTCCAGCACAACCTAGAAGTACTCCTAGGATTTCTGCCATGAGACCTCTTGCTACAGCA
TACTAAGCTTCTACTGGTGATTATCAGGTTATTTCTGACAAA

Alignment

ORF - retro_nleu_2019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.69 %
• Parental protein coverage: 75.98 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VADAMAAFAVEPQGPALGSEPMMLGSPTSPKPGVNAQFLPGFLMGDLPAPVTPQPRSISGPSVGVMEMRS
          VAD.MAAFA.E.Q.PALGSEPMML.S..SPKPGVNAQF.PGF.M..LPA.VTPQP.SISGP..GVMEMRS
Retrocopy VADTMAAFAMELQAPALGSEPMMLAS--SPKPGVNAQF*PGF*MRNLPALVTPQPQSISGPLIGVMEMRS

Parental  PLLAGGSPPQPVVPAHKDKSGAPPVRSIYDDISSPGLGSTPLTSRRQPNIS-VMQSPLVGVTSTPGTGQS
          PLLAGGSPPQPVV.A.KDKSGAP.VRSIYDDISS.GLGSTPLTSRRQP.IS..MQS.L.GVTSTPGTGQS
Retrocopy PLLAGGSPPQPVVLAQKDKSGAPQVRSIYDDISSLGLGSTPLTSRRQPDIS<IMQSSLTGVTSTPGTGQS

Parental  MFSPASIGQPRKTTLSPAQLDPFYTQGDSLTSEDHLDDSWVTVFGFPQASASYILLQFAQYGNILKHVMS
          MFSPA.IGQP.K.TLSP.QLD.FYTQGDSLTSEDHLDD.WVTVFGF.QASASYILLQFAQYGNILKH.MS
Retrocopy MFSPANIGQP*KMTLSPSQLDSFYTQGDSLTSEDHLDDTWVTVFGFSQASASYILLQFAQYGNILKHMMS

Parental  NTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKSVMESSDR-CALSSPSLAFTPPIKTLGTP
          NTGN...I.YQSKLQA.KAL.KDGRIF.E.I.IGVKPCID.SVM.S.DR...LSSPS.AFTPPIKTLGTP
Retrocopy NTGN*LYIHYQSKLQAWKALTKDGRIFREFIVIGVKPCID*SVMGSTDR<TCLSSPSFAFTPPIKTLGTP

Parental  TQPGSTPRISTMRPLATAYKASTSDYQVISDR
          .QP.STPRIS.MRPLATAY.AST.DYQVISD.
Retrocopy AQPRSTPRISAMRPLATAY*ASTGDYQVISDK

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_2019 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.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008469	1 retrocopy	retro_eeur_666,
Homo sapiens	ENSG00000163002	1 retrocopy	retro_hsap_551,
Gorilla gorilla	ENSGGOG00000009919	1 retrocopy	retro_ggor_500,
Macaca mulatta	ENSMMUG00000004140	1 retrocopy	retro_mmul_2387,
Nomascus leucogenys	ENSNLEG00000006423	1 retrocopy	retro_nleu_2019 ,
Pongo abelii	ENSPPYG00000012998	1 retrocopy	retro_pabe_508,
Pan troglodytes	ENSPTRG00000012711	1 retrocopy	retro_ptro_414,
Ictidomys tridecemlineatus	ENSSTOG00000000711	2 retrocopies	retro_itri_755, retro_itri_760,