RetrogeneDB ID: retro_nleu_1710

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397306.1:4086099..4086774(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS2
• Ensembl ID: ENSNLEG00000016949
• Aliases: None
• Description: None

Sequence

>retro_nleu_1710
ATGGCAGCAGCAGCTGATCAGGGTGGGAGAAGTGGTGGTAGTGGAGGCAGTAGTGGGGCTGGCGGTGGTTCCAGGTGCGG
GACAGGCAGTGGCCATAGCGGCTTGCTGGATAAGTGGAAGATAGATGATAAGCCTGTAAAAATTGACGAGTGGGATGGAT
TAGCTGTGAAAAACTCTTTGGATGATTCTGCCAAAAAGTTACTTCTGGAAAAATAAAAATATGTGGAGAATTTTGGTCTC
ATTGATGGTCGCCTCACCATCTGTACAATCTCCTGTTTCTTTGCCATAGTGGCTTTGATTTGGGATTATATGCACCCCTT
TCCATAGTCCAAACCCATTTTGGCTTTGTGCATCATATCCTATTTTATGATGATGGCGATTCTGACCATTTATACCTCAT
ATAAGGACAGGAGCATCTTTCTCGTGGCCCACAGGAAAGATCCTATAGGAATGGATCCTGATGATATTTGGCAACTGTCC
TCCAGTCTTAAAAGGTTTGATGACAAATACACCTCGAAGCTGACCTTCATCAGTGGGAGAACAAAGCAGCAGCGGGAAGC
CGAGTTCACCAAGTCCATTGCTAAGTTTTTTGACCACAGTGGGACACTGGTCATGGATGCACATGAGCCTGAAATATCCA
AGCTCCATGGCAGTCTCGCCATAGAAAGAAAAATA

Alignment

ORF - retro_nleu_1710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.78 %
• Parental protein coverage: 99.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAVATQSGRSGGSGGCSGAGGASNCGTGSGRSGLLDKWKIDDKPVKIDKWDGSAVKNSLDDSAKKVLLE
          MAA.A.Q.GRSGGSGG.SGAGG.S.CGTGSG.SGLLDKWKIDDKPVKID.WDG.AVKNSLDDSAKK.LLE
Retrocopy MAAAADQGGRSGGSGGSSGAGGGSRCGTGSGHSGLLDKWKIDDKPVKIDEWDGLAVKNSLDDSAKKLLLE

Parental  KYKYVENFGLIDGRLTICTISCFFAIVALIWDYMHPFPESKPVLALCVISYFVMMGILTIYTSYKEKSIF
          K.KYVENFGLIDGRLTICTISCFFAIVALIWDYMHPFP.SKP.LALC.ISYF.MM.ILTIYTSYK..SIF
Retrocopy K*KYVENFGLIDGRLTICTISCFFAIVALIWDYMHPFP*SKPILALCIISYFMMMAILTIYTSYKDRSIF

Parental  LVAHRKDPTGMDPDDIWQLSSSLKRFDDKYTLKLTFISGRTKQQREAEFTKSIAKFFDHSGTLVMDAYEP
          LVAHRKDP.GMDPDDIWQLSSSLKRFDDKYT.KLTFISGRTKQQREAEFTKSIAKFFDHSGTLVMDA.EP
Retrocopy LVAHRKDPIGMDPDDIWQLSSSLKRFDDKYTSKLTFISGRTKQQREAEFTKSIAKFFDHSGTLVMDAHEP

Parental  EISRLHDSLAIERKI
          EIS.LH.SLAIERKI
Retrocopy EISKLHGSLAIERKI

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_1710 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 21 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017127	1 retrocopy	retro_amel_1372,
Choloepus hoffmanni	ENSCHOG00000002974	3 retrocopies	retro_chof_1392, retro_chof_1588, retro_chof_2300,
Callithrix jacchus	ENSCJAG00000015576	2 retrocopies	retro_cjac_1500, retro_cjac_1929,
Cavia porcellus	ENSCPOG00000007273	2 retrocopies	retro_cpor_438, retro_cpor_578,
Dipodomys ordii	ENSDORG00000009679	1 retrocopy	retro_dord_423,
Homo sapiens	ENSG00000118363	4 retrocopies	retro_hsap_1488, retro_hsap_3137, retro_hsap_360, retro_hsap_723,
Gorilla gorilla	ENSGGOG00000014500	3 retrocopies	retro_ggor_1141, retro_ggor_372, retro_ggor_610,
Microcebus murinus	ENSMICG00000011153	2 retrocopies	retro_mmur_1566, retro_mmur_656,
Macaca mulatta	ENSMMUG00000010685	1 retrocopy	retro_mmul_26,
Monodelphis domestica	ENSMODG00000007130	2 retrocopies	retro_mdom_1127, retro_mdom_1454,
Mus musculus	ENSMUSG00000035227	1 retrocopy	retro_mmus_2088,
Nomascus leucogenys	ENSNLEG00000016949	2 retrocopies	retro_nleu_1710 , retro_nleu_470,
Otolemur garnettii	ENSOGAG00000015621	1 retrocopy	retro_ogar_2649,
Ochotona princeps	ENSOPRG00000014459	2 retrocopies	retro_opri_266, retro_opri_948,
Pongo abelii	ENSPPYG00000003682	4 retrocopies	retro_pabe_1237, retro_pabe_2619, retro_pabe_2817, retro_pabe_625,
Pan troglodytes	ENSPTRG00000004073	1 retrocopy	retro_ptro_1007,
Rattus norvegicus	ENSRNOG00000018164	2 retrocopies	retro_rnor_2078, retro_rnor_2168,
Sarcophilus harrisii	ENSSHAG00000005389	1 retrocopy	retro_shar_787,
Sus scrofa	ENSSSCG00000014850	1 retrocopy	retro_sscr_648,
Ictidomys tridecemlineatus	ENSSTOG00000012647	2 retrocopies	retro_itri_1283, retro_itri_1584,
Tursiops truncatus	ENSTTRG00000005830	3 retrocopies	retro_ttru_1478, retro_ttru_1496, retro_ttru_1867,