RetrogeneDB ID: retro_ptro_1910

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:98701777..98702538(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD2
• Ensembl ID: ENSPTRG00000012081
• Aliases: None
• Description: None

Sequence

>retro_ptro_1910
GGAATCACCAGTGAGACAATTGTGAAACCAGCTTCAATTTCTGAGGAAGAATTGTTGAAGTTAATAAATAAACTGAGTAA
TGTTGATAATTAGATGGCCACCTTGTTCAGCTGCCTCTTCCAGAGCACACTGATGAGAGAAAGATCTGCAATGCTTTTTC
TCCAGACAAGGATGTTGATGGCTTTCCTGTAATGAATGTAGGACAAAAGTGTTTGGACCAATATTCCATGTTACCGGCTA
CCCCATGGGGTGTGTAGGAAATAATTAAGCGAACTGACATTCCAACCTTAGGGAAGAATGTGGTTGTGACTGGAAGGTCA
AAAATTGTTGGAATGCCCATTGTAATGTCACTGCACATACGTGGGGTGCATGAACGTCCCAGATATGATGCCACCGTTAC
AATATCTCATGGATATACTCCCAAAGAGCAGTTGAAGAAACAGAATTTTTGCAGATATTGTAAGATCCGCTGCAGGAATT
CTAAACCTGTTCACAATAGATATAATCAAGGAAAAAACAGCAGTTATTGATGTGGGAATAACTAGAGTTCAAGATCCCGT
AACTGCTAAACCCAAATTGGTTGGAGACATGGATTTTGAAGGAGTCAGATAAAAAGCCGGTTACATCAGGCCACTTCCTG
GAGGTGTTGGCCTCATGACGGTGGCGATGCTAATGAAGAATACCATTATTGTTGCAAAAAAGTGCTGAGGCTTGAAGAAC
AGTAAGTGCTGACGTCTAAAGAGCTTGGAGTAGCCACTAAT

Alignment

ORF - retro_ptro_1910 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.68 %
• Parental protein coverage: 72.86 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GINSETIMKPASISEEELLNLINKLNNDDN-VDGLLVQLPLPEHIDERRICNAVSPDKDVDGFHVINVGR
          GI.SETI.KPASISEEELL.LINKL.N.DN..DG.LVQLPLPEH.DER.ICNA.SPDKDVDGF.V.NVG.
Retrocopy GITSETIVKPASISEEELLKLINKLSNVDN<LDGHLVQLPLPEHTDERKICNAFSPDKDVDGFPVMNVGQ

Parental  MCLDQYSMLPATPWGVWEIIKRTGIPTLGKNVVVAGRSKNVGMPIAMLLHTDGAHERPGGDATVTISHRY
          .CLDQYSMLPATPWGV.EIIKRT.IPTLGKNVVV.GRSK.VGMPI.M.LH..G.HERP..DATVTISH.Y
Retrocopy KCLDQYSMLPATPWGV*EIIKRTDIPTLGKNVVVTGRSKIVGMPIVMSLHIRGVHERPRYDATVTISHGY

Parental  T-PKEQLKKHTILADIVISAAGIPNLITADMIKEGAAVIDVGINRVHDPVTAKPKLVGDVDFEGVRQKAG
          T.PK.......I.ADIV.SAAGI.NL.T.D.IKE..AVIDVGI.RV.DPVTAKPKLVGD.DFEGVR.KAG
Retrocopy T>PKSS*RNR-IFADIVRSAAGILNLFTIDIIKEKTAVIDVGITRVQDPVTAKPKLVGDMDFEGVR*KAG

Parental  YITPVPGGVGPMTVAMLMKNTIIAA-KKVLRLEEREVLKSKELGVATN
          YI.P.PGGVG.MTVAMLMKNTII.A.KKVLRLEE..VL.SKELGVATN
Retrocopy YIRPLPGGVGLMTVAMLMKNTIIVA<KKVLRLEEQ*VLTSKELGVATN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.02 RPM	2.57 RPM
SRP007412_cerebellum	0.00 RPM	6.13 RPM
SRP007412_heart	0.00 RPM	13.73 RPM
SRP007412_kidney	0.03 RPM	11.53 RPM
SRP007412_liver	0.00 RPM	3.04 RPM
SRP007412_testis	0.00 RPM	24.13 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1910 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1910 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1910 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2817

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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,