RetrogeneDB ID: retro_nleu_2286

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397341.1:4960761..4961423(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000013344
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HAX1
• Ensembl ID: ENSNLEG00000011290
• Aliases: None
• Description: None

Sequence

>retro_nleu_2286
GAGGAATTTGGCTTTGGCTTCAGCTTCAGCCCAGAAGGAGGGATACGTTTCCACGATAACTTCGGCTTTGATGACCTAGT
ACAAGATTTCAATAGCATCTTCAGCAATATGGGGGCCTGGACCTTGCCTTCCCATCCTCCTGAACTTCCAGGTTCTGAGT
CAGAGACACCTGGTGAGAGACTGCAGGAGGGACAGGCACTTCGAGAATCAATGCTTAAGTATCCAGATAGTCACCAGCCC
AGGATCTTTGAGAGGGTCTTGGAGAGTGATGCAAGAAGTGAATCCCCCAAACCAGCACCAGACTGGGGTTCCCAGAGACC
ATTTCATAGGTTTGATGACATATGGCCTGTGGACCCCCATCCTAGAGCCAGAGAGGACAATGATCTTGATTCCCGGGTTT
CCCAGGAGGGTCTTGGCCCGGTTCTACAGCCCCAGCCCAGATCCTATTTCAAGAGCATCTCTGTGACGAAGATCACTAAG
CCAGATGGGATAGTGGAGGAGCACTTGACTGTGGTGGACAGTGAGGGCCAGACAGAGACCACCGTAACCCAACACGAAGC
AGATAGCAGTCCTAGGATGATCCAGAATCACCAAGACCTCCAGCCCTGGATGATGCCTTCTCCACCCTGGACTTATTCCT
AGGACTTCGGTTCCAGTCCCGG

Alignment

ORF - retro_nleu_2286 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.63 %
• Parental protein coverage: 79.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEFGFGFSFSPGGGIRFHDNFGFDDLVRDFNSIFSDMGAWTLPSHPPELPGPESETPGERLREGQTLRDS
          EEFGFGFSFSP.GGIRFHDNFGFDDLV.DFNSIFS.MGAWTLPSHPPELPG.ESETPGERL.EGQ.LR.S
Retrocopy EEFGFGFSFSPEGGIRFHDNFGFDDLVQDFNSIFSNMGAWTLPSHPPELPGSESETPGERLQEGQALRES

Parental  MLKYPDSHQPRIFGGVLETPQVIQPPWPPKVLELQVPPFSFDDVWPMDPHPRTREDNDLDSQVSQEGLGP
          MLKYPDSHQPRIF..VLE.......P.P......Q.P...FDD.WP.DPHPR.REDNDLDS.VSQEGLGP
Retrocopy MLKYPDSHQPRIFERVLESDARSESPKPAPDWGSQRPFHRFDDIWPVDPHPRAREDNDLDSRVSQEGLGP

Parental  VLQPQPKSYFKSISVTTITKPDGIVEERRTVVDSEGRTETTVTRHEADSSPR-GDPESPRPPALDDAFSI
          VLQPQP.SYFKSISVT.ITKPDGIVEE..TVVDSEG.TETTVT.HEADSSPR..DPESPRPPALDDAFS.
Retrocopy VLQPQPRSYFKSISVTKITKPDGIVEEHLTVVDSEGQTETTVTQHEADSSPR<DDPESPRPPALDDAFST

Parental  LDLFLGRWFRSR
          LDLFLG..F.SR
Retrocopy LDLFLGLRFQSR

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_2286 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009660	1 retrocopy	retro_cjac_1888,
Dasypus novemcinctus	ENSDNOG00000016727	1 retrocopy	retro_dnov_1537,
Dipodomys ordii	ENSDORG00000012587	1 retrocopy	retro_dord_769,
Homo sapiens	ENSG00000143575	1 retrocopy	retro_hsap_4912,
Microcebus murinus	ENSMICG00000010414	2 retrocopies	retro_mmur_1118, retro_mmur_1284,
Monodelphis domestica	ENSMODG00000017215	1 retrocopy	retro_mdom_433,
Mus musculus	ENSMUSG00000027944	3 retrocopies	retro_mmus_1306, retro_mmus_2000, retro_mmus_353,
Nomascus leucogenys	ENSNLEG00000011290	1 retrocopy	retro_nleu_2286 ,
Pan troglodytes	ENSPTRG00000001380	1 retrocopy	retro_ptro_3275,
Rattus norvegicus	ENSRNOG00000045647	1 retrocopy	retro_rnor_736,
Tupaia belangeri	ENSTBEG00000014445	1 retrocopy	retro_tbel_930,