RetrogeneDB ID: retro_ptro_2641

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:83099223..83100016(-)
• 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_2641
ACTCATGTCCTCAACAAAACCAGGGCAGCTGCAGATGTGGTAATCAATGGTGAGACGATTATGAAACCAGCTTCAATTTC
AGAGGAAGAATTGTTGAATTTAATCAATAAACTGAATAATAATGTAGATGGCCTTATTCAGCTGCCTCTTCCAGGCATAT
TGATGATAGAAAGACCTGTAATGCCTTTCTCCAGACAAGGATGTCAATGACTTTCATGTAATTAATATAGGGCGAATATG
TTTGGACCAGTATTCCACGTTACTAGCTACCCCATGGGGTGTGTGGGAAATAATTAAGTAAACTGGCATTCCCACCCTAG
GGAAGAATGTGGTTGTGGCTGGAAGGTCAAAAAATGTTGAAATGCCAATTGCAATGTTACTGCACACAGATGGGGCACAT
GAAGGTCCCAGAGGTGATGCTACTGTTACAATATCTCATGGATACACTCCCAAAGAGCAGCTGAAGAAACATACCATTCT
TGCAGATATTGTAATATCTGCTGCAGGCATTCCAAATCTCTTCACAGCAGATATGATCAAGGAAGGAGCAGCCATCATTA
ATGTGGGAATAAATAGAGTTCAAGATCCCATAACTGCAAACCCAAGTTAGTTGGAGATGTGGATTTTGAAGGAGTCAGAC
AAAAAGCTGGTTATATCACTCCAGTTCCTGGAGGTGTTGGCCCCAAAACAGTGGTGATGCTAATGAAGAATACCATTATT
ACTGCAAAAAAAAATGCTGAGGCATGAAGAACGAGAAGTGTTGACGTCTAAAGAGCTTGAAGTTGCCACTAAT

Alignment

ORF - retro_ptro_2641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.82 %
• Parental protein coverage: 76.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SYVLNKTRAAAAVGINSETIMKPASISEEELLNLINKLNNDDNVDGLLVQLPLP-EHIDERRICNA-VSP
          ..VLNKTRAAA.V.IN.ETIMKPASISEEELLNLINKLNN..NVDGL..QLPLP..HID.R..CNA..SP
Retrocopy THVLNKTRAAADVVINGETIMKPASISEEELLNLINKLNN--NVDGL-IQLPLP<RHIDDRKTCNA<LSP

Parental  DKDVDGFHVINVGRMCLDQYSMLPATPWGVWEIIKRTGIPTLGKNVVVAGRSKNVGMPIAMLLHTDGAHE
          DKDV..FHVIN.GR.CLDQYS.L.ATPWGVWEIIK.TGIPTLGKNVVVAGRSKNV.MPIAMLLHTDGAHE
Retrocopy DKDVNDFHVINIGRICLDQYSTLLATPWGVWEIIK*TGIPTLGKNVVVAGRSKNVEMPIAMLLHTDGAHE

Parental  RPGGDATVTISHRYTPKEQLKKHTILADIVISAAGIPNLITADMIKEGAAVIDVGINRVHDPVTA-KPKL
          .P.GDATVTISH.YTPKEQLKKHTILADIVISAAGIPNL.TADMIKEGAA.I.VGINRV.DP.TA.KPKL
Retrocopy GPRGDATVTISHGYTPKEQLKKHTILADIVISAAGIPNLFTADMIKEGAAIINVGINRVQDPITA<KPKL

Parental  VGDVDFEGVRQKAGYITPVPGGVGPMTVAMLMKNTIIA-AKKVLRLEEREVLKSKELGVATN
          VGDVDFEGVRQKAGYITPVPGGVGP.TV.MLMKNTII......LR.EEREVL.SKEL.VATN
Retrocopy VGDVDFEGVRQKAGYITPVPGGVGPKTVVMLMKNTIIT>XXXXLRHEEREVLTSKELEVATN

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	0.00 RPM	2.57 RPM
SRP007412_cerebellum	0.04 RPM	6.13 RPM
SRP007412_heart	0.00 RPM	13.73 RPM
SRP007412_kidney	0.00 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_2641 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2641 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2641 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_3078

---

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,