RetrogeneDB ID: retro_nleu_147

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: ADFV01139425.1:11712..12101(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM183A
• Ensembl ID: ENSNLEG00000013230
• Aliases: None
• Description: None

Sequence

>retro_nleu_147
ATGGCAGGACACCCCAGGGAGAAGGTGATCCAGGGTGAGGTCCGTCAGAACCAGATCTTGCAGGAGCTGTACCTCAAAGA
GCTACCAGCCCAGAACGTCTATGCGTGGCATCACGTGAACCCCTCCACGAGGTCCACAGATCACCAGGAAGCCCACGTCT
TGGCATGGTAACCTGGAGGAGCCTGGAGACACCAGGTTTCAGAATCTCATTCGCCACGCTGCCCAGGGACCAAGGAAGAA
GGACCCAGACACAGACTGAAAACCAGGAAACTGCATGGGACTCAGAGCCCTGACTCAACCCAGAACGCCCAGATCGCAGG
CTCAACCACTGCAGGGTCTGCAGTGACATCGCTCTGTACAAGGCTCAGATGTGGAGCCTGGGAGAAGAT

Alignment

ORF - retro_nleu_147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 97.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAGHPRQKVIPDEVHQNQILRELYLKELRTQKLYTQYHVNP-LRKIHT-VTRKPMSWHDNLEEPADARFL
          MAGHPR.KVI..EV.QNQIL.ELYLKEL..Q..Y...HVNP.L...H...TRKP.SWH.NLEEP.D.RF.
Retrocopy MAGHPREKVIQGEVRQNQILQELYLKELPAQNVYAWHHVNP<LHEVHR<ITRKPTSWHGNLEEPGDTRFQ

Parental  NLIHHAAQ-GPRKKYP-ETQTENQEVGWDLEPLINPERHDRRLNHFRVCSDITLYKAKTWGLGDD
          NLI.HAAQ.G.....P..TQTENQE..WD.EP..NPER.DRRLNH.RVCSDI.LYKA..W.LG.D
Retrocopy NLIRHAAQ<GTKEEGP<QTQTENQETAWDSEP*LNPERPDRRLNHCRVCSDIALYKAQMWSLGED

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_147 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
Canis familiaris	ENSCAFG00000005339	1 retrocopy	retro_cfam_671,
Callithrix jacchus	ENSCJAG00000003315	1 retrocopy	retro_cjac_323,
Homo sapiens	ENSG00000186973	1 retrocopy	retro_hsap_1,
Gorilla gorilla	ENSGGOG00000010892	2 retrocopies	retro_ggor_1704, retro_ggor_69,
Nomascus leucogenys	ENSNLEG00000013230	3 retrocopies	retro_nleu_147 , retro_nleu_2537, retro_nleu_2865,
Pongo abelii	ENSPPYG00000001457	1 retrocopy	retro_pabe_48,
Pan troglodytes	ENSPTRG00000000624	1 retrocopy	retro_ptro_22,