RetrogeneDB ID: retro_nleu_2877

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397458.1:1689963..1690520(-)
• Located in intron of: ENSNLEG00000014509

Retrocopy information

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

Parental gene information

• Parental gene symbol: TWF1
• Ensembl ID: ENSNLEG00000017931
• Aliases: None
• Description: None

Sequence

>retro_nleu_2877
GCAAGTGAGGATGTTAAAGAGATCTTGCCAGAGCCAGAAATGGAAAGTACAGACTTCTGAAAATATCTATTGAAAATGAG
CAACTTATGATTGGATCATATAGTCAGCCTTCAGATTCCTGGGATAAGGATTATGATTCCTTTGTTTTACCCCTGTTGGA
GGACAAACAACTGTGCTATATATTATTCAGGTTAGATTCTCAGAATGCCCAGGGATATGAATGAATATTCATTGCATGGT
TTCCAGATCATTCTCATGTCCGTCAAAAAAGTTGTATGCAGCAACAAGAGCAACTCTGGAAAAGGAATCTGGAGGTGGCC
GCGTTAAAGATGAAGTATTTGGAACAGTAAAGGAAGATGTATCATTCCATGGATATAAAAAATGTTTGCTGTCACAATCT
TCCCCTGCCCTACTGACTGCAGCTGAGGAAGAATTATGACATTAAAATCAATGAGGTACAGACTGACGTGGGTGTGGACA
CTAAGCATCAAACACTACAAGGAGTAGCATTTCCTATTTCTCGAGAAGCCTTTCAGGCTTTGGAAAAAATGAATAAC

Alignment

ORF - retro_nleu_2877 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.42 %
• Parental protein coverage: 53.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASEDVKEIF-ARARNGKYRLLKISIENEQLVIGSYSQPSDSWDKDYDSFVLPLLEDKQPCYILFRLDSQN
          ASEDVKEI..ARARNGKYRLLKISIENEQL.IGSYSQPSDSWDKDYDSFVLPLLEDKQ.CYILFRLDSQN
Retrocopy ASEDVKEIL<ARARNGKYRLLKISIENEQLMIGSYSQPSDSWDKDYDSFVLPLLEDKQLCYILFRLDSQN

Parental  AQGYEWIFIAWSPDHSHVRQKM-LYAATRATLKKEFGGGHIKDEVFGTVKEDVSLHGYKKYLLSQSSPAP
          AQGYE.IFIAW.PDHSHVRQK..LYAATRATL.KE.GGG..KDEVFGTVKEDVS.HGYKK.LLSQSSPA.
Retrocopy AQGYE*IFIAWFPDHSHVRQKS<LYAATRATLEKESGGGRVKDEVFGTVKEDVSFHGYKKCLLSQSSPAL

Parental  LTAAEEELR-QIKINEVQTDVGVDTKHQTLQGVAFPISREAFQALEKLNN
          LT.A.EE....IKINEVQTDVGVDTKHQTLQGVAFPISREAFQALEK.NN
Retrocopy LT-AAEEEL>DIKINEVQTDVGVDTKHQTLQGVAFPISREAFQALEKMNN

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_2877 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017332	1 retrocopy	retro_amel_1224,
Choloepus hoffmanni	ENSCHOG00000008386	5 retrocopies	retro_chof_1525, retro_chof_2013, retro_chof_2569, retro_chof_391, retro_chof_509,
Homo sapiens	ENSG00000151239	2 retrocopies	retro_hsap_1819, retro_hsap_4916,
Monodelphis domestica	ENSMODG00000018535	1 retrocopy	retro_mdom_167,
Mustela putorius furo	ENSMPUG00000000364	1 retrocopy	retro_mputfur_1629,
Mus musculus	ENSMUSG00000022451	1 retrocopy	retro_mmus_2961,
Nomascus leucogenys	ENSNLEG00000017931	1 retrocopy	retro_nleu_2877 ,
Otolemur garnettii	ENSOGAG00000007525	1 retrocopy	retro_ogar_1058,
Pan troglodytes	ENSPTRG00000004846	1 retrocopy	retro_ptro_3279,
Rattus norvegicus	ENSRNOG00000022507	1 retrocopy	retro_rnor_2176,