RetrogeneDB ID: retro_nleu_2828

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397443.1:2268942..2269606(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM8A1
• Ensembl ID: ENSNLEG00000001130
• Aliases: None
• Description: None

Sequence

>retro_nleu_2828
GAAGTGTCCGAAGCTGCGGCGCCGTGGGAGGGGCTGGCGCGGCTGAGCGCCCTTAGGTGCTCCTGGCGAGTGCACGAGTG
GCTGTGGCAGTCCTGCTGCGGCTACCTCACCTGGCGCAGCGGCCCGGCCAGCTTCTCCACCTGCTGCAGCTCCCAACCAT
CCCCGCAGAGCTGCCCTTTGGGAGGCACTGCGGTCCCCCGGGCCGCGGCGCCGCCATCCCGCGGCTGTGCTATTACACCC
CCTTCTACTTCCTGAGCCCCAGGGCCGCGGGGGCCTGACCCGGGGGGGCAGCTGCTGGCATCAGCACCCCTGCTCCAGTC
ACGGGCCTGGGACCCTGGGTTCCTTATGCGCAGGCATCCGTCCGGGCCACTCCAGTGACAAAAGTAGGATCTGCAGCCCC
TTCGCGAAGCCCGAGTGAGACCAGGCAACAGGCAGGCAAAGAATATGTTATTCCATCCTTGGGCCACAGGTGGCAAGGAT
GGTGGATTTCTTTATTCTCTTCTTTGTAAAAGCAACCATTGTCTTAAGCATTATGCACCTCAGTGGGATAAAGGGTATCT
CTAAGTTTGCTGTGCATTATATAATGGGAGAAATAGATGAGGACACATCACTGGAAGACTTGTAGCAAATGATAGTTGTG
GCTCTTAGATACAGATTATTAGTT

Alignment

ORF - retro_nleu_2828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.78 %
• Parental protein coverage: 53.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EAPEAAAPRERPARLSAREYSRQVHEWLWQSYCGYLTWHSGLAAFPAYCSPQPSPHSFPSSGAAVPQAAV
          E..EAAAP.E..ARLSA...S..VHEWLWQS.CGYLTW.SG.A.F...CS.QPSP.S.P..G.AVP.AA.
Retrocopy EVSEAAAPWEGLARLSALRCSWRVHEWLWQSCCGYLTWRSGPASFSTCCSSQPSPQSCPLGGTAVPRAAA

Parental  PPP-PQLGYYNPFYFLSPGAAGPDPR-TAAGISTPAPVAGLGPRAPHVQASVRATPVTRIGSAAPSRSPS
          PP..P.L.YY.PFYFLSP.AAG..P...AAGISTPAPV.GLGP..P..QASVRATPVT..GSAAPSRSPS
Retrocopy PPS<PRLCYYTPFYFLSPRAAGA*PGGAAAGISTPAPVTGLGPWVPYAQASVRATPVTKVGSAAPSRSPS

Parental  ETGRQ-AGREYVIPSLAHRFMAEMVDFFILFFIKATIVLSIMHLSGIKDISKFAMHYIIEEIDEDTSMED
          ET.RQ..GR.....S......A.MVDFFILFF.KATIVLSIMHLSGIK.ISKFA.HYI..EIDEDTS.ED
Retrocopy ET-RQ<TGRQRICYSILGPQVARMVDFFILFFVKATIVLSIMHLSGIKGISKFAVHYIMGEIDEDTSLED

Parental  LQKMMVVALIYRLLV
          L..M.VVAL.YRLLV
Retrocopy L*QMIVVALRYRLLV

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_2828 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000137414	2 retrocopies	retro_hsap_2166, retro_hsap_4922,
Macaca mulatta	ENSMMUG00000001992	1 retrocopy	retro_mmul_904,
Monodelphis domestica	ENSMODG00000024641	1 retrocopy	retro_mdom_1866,
Nomascus leucogenys	ENSNLEG00000001130	2 retrocopies	retro_nleu_2828 , retro_nleu_460,
Pan troglodytes	ENSPTRG00000017751	2 retrocopies	retro_ptro_1652, retro_ptro_3296,