RetrogeneDB ID: retro_nleu_595

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397268.1:33365957..33366931(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD2
• Ensembl ID: ENSNLEG00000000326
• Aliases: None
• Description: None

Sequence

>retro_nleu_595
ATGGCTGCGACTTCCCTCATGTCCACGTTGGCTGCCCGGCTGCTGCAGCCCGTGCACAGCTGCTCCCTCCGCCCTCGCCC
CTTCCACCTCGCGGCAGTTCAAGATGAAGCTGTTGTAATTTCTGGAAGGAAACTGGCCCAGCAGATCAAGCAGGAAGTGC
AGCAGGAGGTAGAAGAGTGGGTGGCCTCAGGCGACAAACGGCCACACCTGAGCGTGATCCTCGTTGGCGAGAATTCTGCA
AGTCACTCCTACGTCCTCAACAAAACCAGGGCAGCTGCAGATGTGGGAATCAACAGTGAGACAATTGTGAAACCAGCTTC
AATTTCAGAGGAAGAATTGTTGAATTTAATCAGTAAACTGAATAATGATGATAATGTAGATGGCCTCCTTGTTCAGCTGC
CTCTTCCAGAGCATATTGATGAGAGAAGGATCTGCAATGCTGTTTCTCCAGACAAGGATGCTGATGGCTTTCATGTAATT
AATGTAGGGCGAATGTGTTTGGACCAGTATTCCACCTTACCAGCTACCCCATGGGGTGTGTGGGAAATAATTAAGCGAAC
TGACATTCCAACCCTAGGGAAGAATGTGGTTGTGGCTGGAAGGTCAAAAAATGTTGAAATGCCCATTGCAATGTTACTGT
ACACAGATGGAGCTCATGAACGTCCCGGAGTGATGCCACTGTTACAATATCTCATCTGTATACTCCCACAGAGCAGTTGA
AGAAACATACAATTCTTGCAGATATTGTAATATCTGCTGCAGGTATTCCAAATCTGATTACAGCAAATATGATCAAGGAA
GAAGCAGCAGTCATTGATGTGGGAATAAATGGAGTTCATGATCCTGTAACTGCCAAACCCAAGTTGGTTGGAGATACGGA
TTTTGAAGGAGTCAGACAAAAAGCTGGTTATATCACTCCAGTTCCTGGAGGTGTTGGCCCCATGACAGTGGCAATGCTAA
TGAAGAATACCATT

Alignment

ORF - retro_nleu_595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.94 %
• Parental protein coverage: 93.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAATSLMSALAARLLQPTHSCSLRLRSFHLAAVRNEAVVISGRKLAQQIKQEVRQEVEEWVASGNKRPHL
          MAATSLMS.LAARLLQP.HSCSLR.R.FHLAAV..EAVVISGRKLAQQIKQEV.QEVEEWVASG.KRPHL
Retrocopy MAATSLMSTLAARLLQPVHSCSLRPRPFHLAAVQDEAVVISGRKLAQQIKQEVQQEVEEWVASGDKRPHL

Parental  SVILVGENPASHSYVLNKTRAAADVGINSETIVKPASISEEELLNLINKLNNDDNVDGLLVQLPLPEHID
          SVILVGEN.ASHSYVLNKTRAAADVGINSETIVKPASISEEELLNLI.KLNNDDNVDGLLVQLPLPEHID
Retrocopy SVILVGENSASHSYVLNKTRAAADVGINSETIVKPASISEEELLNLISKLNNDDNVDGLLVQLPLPEHID

Parental  ERRICNAVSPDKDVDGFHVINVGRMCLDQYSMLPATPWGVWEIIKRTGIPTLGKNVVVAGRSKNVGMPIA
          ERRICNAVSPDKD.DGFHVINVGRMCLDQYS.LPATPWGVWEIIKRT.IPTLGKNVVVAGRSKNV.MPIA
Retrocopy ERRICNAVSPDKDADGFHVINVGRMCLDQYSTLPATPWGVWEIIKRTDIPTLGKNVVVAGRSKNVEMPIA

Parental  MLLHTDGAHERPG-GDATVTISHRYTPKEQLKKHTILADIVISAAGIPNLITADMIKEGAAVIDVGINRV
          MLL.TDGAHERPG..DATVTISH.YTP.EQLKKHTILADIVISAAGIPNLITA.MIKE.AAVIDVGIN.V
Retrocopy MLLYTDGAHERPG<SDATVTISHLYTPTEQLKKHTILADIVISAAGIPNLITANMIKEEAAVIDVGINGV

Parental  HDPVTAKPKLVGDVDFEGVRQKAGYITPVPGGVGPMTVAMLMKNTI
          HDPVTAKPKLVGD.DFEGVRQKAGYITPVPGGVGPMTVAMLMKNTI
Retrocopy HDPVTAKPKLVGDTDFEGVRQKAGYITPVPGGVGPMTVAMLMKNTI

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_595 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 10 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017345	2 retrocopies	retro_amel_1098, retro_amel_1584,
Canis familiaris	ENSCAFG00000008716	1 retrocopy	retro_cfam_580,
Callithrix jacchus	ENSCJAG00000017810	3 retrocopies	retro_cjac_2225, retro_cjac_2568, retro_cjac_3078,
Homo sapiens	ENSG00000065911	5 retrocopies	retro_hsap_2732, retro_hsap_2817, retro_hsap_3002, retro_hsap_3309, retro_hsap_3874,
Macropus eugenii	ENSMEUG00000013987	4 retrocopies	retro_meug_1468, retro_meug_152, retro_meug_1577, retro_meug_2074,
Mustela putorius furo	ENSMPUG00000007829	3 retrocopies	retro_mputfur_1087, retro_mputfur_1397, retro_mputfur_1551,
Nomascus leucogenys	ENSNLEG00000000326	5 retrocopies	retro_nleu_1196, retro_nleu_207, retro_nleu_2501, retro_nleu_595 , retro_nleu_749,
Otolemur garnettii	ENSOGAG00000009089	1 retrocopy	retro_ogar_3390,
Pan troglodytes	ENSPTRG00000012081	4 retrocopies	retro_ptro_1846, retro_ptro_1910, retro_ptro_2162, retro_ptro_2641,
Pteropus vampyrus	ENSPVAG00000013948	2 retrocopies	retro_pvam_1357, retro_pvam_1414,