RetrogeneDB ID: retro_nleu_3007

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397567.1:190592..190879(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC42
• Ensembl ID: ENSNLEG00000008198
• Aliases: None
• Description: cell division cycle 42 [Source:HGNC Symbol;Acc:1736]

Sequence

>retro_nleu_3007
ATGCAGACAATTAGTGTGTTGTTGTGGGCGATGGTGCTGTTGGTAAAACATGTCTCCTGATATCCTACACAACAAACAAA
TTTTCATCGGAACATGTACCAACTGTTTTTGACAATTATGCAGTCACAGTTATGATTGGTGGAGAACCATATACTCTTGG
GCTTTTTGATACTACAGGGCAGGAGGATTATGACAGATTACTACTACTGAGTTATCCACAGACAGATGTATTTCTAGTCT
GTTTTTCAGTAGTCTCTCCAACTTCATTTGAAAATGTGAAAGAAAAA

Alignment

ORF - retro_nleu_3007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.75 %
• Parental protein coverage: 50.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQTIK-CVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRP
          MQTI..CVVVGDGAVGKTCLLISYTTNKF.SE.VPTVFDNYAVTVMIGGEPYTLGLFDT.GQEDYDRL..
Retrocopy MQTIS<CVVVGDGAVGKTCLLISYTTNKFSSEHVPTVFDNYAVTVMIGGEPYTLGLFDTTGQEDYDRLLL

Parental  LSYPQTDVFLVCFSVVSPSSFENVKEK
          LSYPQTDVFLVCFSVVSP.SFENVKEK
Retrocopy LSYPQTDVFLVCFSVVSPTSFENVKEK

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_3007 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 15 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014707	5 retrocopies	retro_cfam_1587, retro_cfam_1970, retro_cfam_2189, retro_cfam_88, retro_cfam_89,
Choloepus hoffmanni	ENSCHOG00000005306	10 retrocopies	retro_chof_103, retro_chof_1044, retro_chof_1195, retro_chof_1853, retro_chof_2055, retro_chof_2105, retro_chof_2331, retro_chof_2407, retro_chof_50, retro_chof_800,
Callithrix jacchus	ENSCJAG00000005912	6 retrocopies	retro_cjac_1275, retro_cjac_1808, retro_cjac_1826, retro_cjac_2251, retro_cjac_751, retro_cjac_911,
Cavia porcellus	ENSCPOG00000006543	4 retrocopies	retro_cpor_1168, retro_cpor_286, retro_cpor_33, retro_cpor_887,
Echinops telfairi	ENSETEG00000004443	1 retrocopy	retro_etel_2010,
Felis catus	ENSFCAG00000004853	4 retrocopies	retro_fcat_129, retro_fcat_1421, retro_fcat_1579, retro_fcat_896,
Macaca mulatta	ENSMMUG00000022009	8 retrocopies	retro_mmul_1449, retro_mmul_1612, retro_mmul_1685, retro_mmul_1900, retro_mmul_1932, retro_mmul_24, retro_mmul_349, retro_mmul_598,
Monodelphis domestica	ENSMODG00000016078	3 retrocopies	retro_mdom_18, retro_mdom_181, retro_mdom_537,
Mustela putorius furo	ENSMPUG00000015999	2 retrocopies	retro_mputfur_308, retro_mputfur_957,
Nomascus leucogenys	ENSNLEG00000008198	4 retrocopies	retro_nleu_2029, retro_nleu_2949, retro_nleu_3007 , retro_nleu_679,
Nomascus leucogenys	ENSNLEG00000014759	7 retrocopies	retro_nleu_1215, retro_nleu_1330, retro_nleu_2094, retro_nleu_2355, retro_nleu_689, retro_nleu_724, retro_nleu_87,
Oryctolagus cuniculus	ENSOCUG00000009986	1 retrocopy	retro_ocun_60,
Sorex araneus	ENSSARG00000005184	3 retrocopies	retro_sara_10, retro_sara_220, retro_sara_3,
Ictidomys tridecemlineatus	ENSSTOG00000000805	4 retrocopies	retro_itri_1158, retro_itri_1602, retro_itri_1615, retro_itri_431,
Vicugna pacos	ENSVPAG00000006919	3 retrocopies	retro_vpac_13, retro_vpac_451, retro_vpac_542,