RetrogeneDB ID: retro_nleu_1196

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397284.1:2074125..2074886(-)
• 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_1196
GGAATCACCAGTGAGGCAATTGTGAAACCAGCTTCAATTTCTGAGGAAGAATTGTTGAAGTTAATAAATAAACTGAGTAA
TATTGATAATTAGATGGCCACCTTGTTCAGCTACCTCTTCCAGAGCACACTGATGAGAGAAAGATCTGCAATGCTCTTTC
TCCAGACAAGGATGATGATGACTTCTCCGTAATGAATGTAGGACAAAAGTGTTTGGACCAGTATTCCATGTTACCGACTA
CCCCATGGGGTGTGTGGGAAATAATTAAGCGAACTGACATTCCAACCCTAGGAAAGAATGTGGTTGTGACTGGAAGGTCA
AAAGTTGTTGGAATGCCCATTGTGATGTCACTGCACATAGATGGGGCTCATGAACGTCCCAGAGATGATGCCACTGTTAT
AATATCTCACGGATATACTCCCAAAAAGCAGTTGAAGAAACAAAATTTTTGCAGATATTTTAACATCCGCTGCAGGAATT
CCAAACCTGTTCACAATAGATATAATCAAGGAAAGAGCAGCAGTTACTGATGTGGGAATAACTAGAGTTCAAGATCCCGT
AACTGCTAAACCCAAATTGGTTGGAGACGTGGATTTTGAAGGAGTCAGATAAAAAGCCGGTTACATCATGCCACTTCCTG
GAGGTGTTGGCCCCATGACGGTGGCGATGCTAATGAAGAATACCATTATTGCTGCAAAAAAGTGCTGAGGCTTGAAGAAC
AGTAAGTGCTGACGTCTAAAGAGCTTGAAGTAGCCACTAAT

Alignment

ORF - retro_nleu_1196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.07 %
• Parental protein coverage: 72.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GINSETIVKPASISEEELLNLINKLNNDDN-VDGLLVQLPLPEHIDERRICNAVSPDKDVDGFHVINVGR
          GI.SE.IVKPASISEEELL.LINKL.N.DN..DG.LVQLPLPEH.DER.ICNA.SPDKD.D.F.V.NVG.
Retrocopy GITSEAIVKPASISEEELLKLINKLSNIDN<LDGHLVQLPLPEHTDERKICNALSPDKDDDDFSVMNVGQ

Parental  MCLDQYSMLPATPWGVWEIIKRTGIPTLGKNVVVAGRSKNVGMPIAMLLHTDGAHERPGGDATVTISHRY
          .CLDQYSMLP.TPWGVWEIIKRT.IPTLGKNVVV.GRSK.VGMPI.M.LH.DGAHERP..DATV.ISH.Y
Retrocopy KCLDQYSMLPTTPWGVWEIIKRTDIPTLGKNVVVTGRSKVVGMPIVMSLHIDGAHERPRDDATVIISHGY

Parental  T-PKEQLKKHTILADIVISAAGIPNLITADMIKEGAAVIDVGINRVHDPVTAKPKLVGDVDFEGVRQKAG
          T.PK.......I.ADI..SAAGIPNL.T.D.IKE.AAV.DVGI.RV.DPVTAKPKLVGDVDFEGVR.KAG
Retrocopy T>PKSS*R-NKIFADILTSAAGIPNLFTIDIIKERAAVTDVGITRVQDPVTAKPKLVGDVDFEGVR*KAG

Parental  YITPVPGGVGPMTVAMLMKNTIIAAKK-VLRLEEREVLKSKELGVATN
          YI.P.PGGVGPMTVAMLMKNTIIAAKK.VLRLEE..VL.SKEL.VATN
Retrocopy YIMPLPGGVGPMTVAMLMKNTIIAAKK<VLRLEEQ*VLTSKELEVATN

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_1196 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.

---

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,