RetrogeneDB ID: retro_ptro_3223

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:58140086..58142001(-)
• Located in intron of: ENSPTRG00000021960

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD1
• Ensembl ID: ENSPTRG00000006435
• Aliases: None
• Description: methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase [Source:HGNC Symbol;Acc:7432]

Sequence

>retro_ptro_3223
CCCGTTCCTGGTGGCTTAGGGCTCATGACGGTTGCAATGCTCATGCAGAGCACTGTAGAGAGTGCCAAGCTTTTCCTGGA
GAAATTTAAGCCAGGAAAGTGGATGATTCAGTATAACAACCTTAACCTCAAGACACCTGTTCGAAGTGACATTGATATAT
CACGATCTTGTAAACCGAAGCCCATTGGTAAGCTGGCTTGAGGAATTGGTCTGCTGTCTGAAGAGGTAGAATTATATGGT
GAAACAAAGGCCAAAGTTCTGCTGTCAGCACTAGAACGCCTGAAGCACCAACCTGATGGGAAATATCAGGTGTGACTTGA
ATAACTCCAACACCCCTGGGAGAAGGGAAAAGCACGACTACAATCGGGCTGGTGCAAGCCCTTCTTGCCCATCTCTCCCA
GAACTTTTTTATGTGTGTGCGACAGCCTTCTCAGGGCCCCACCTTTGGAATAAAAGGTGGTGCTGCAGGAGGCGGCTACT
CCCAGGTCATTCCTATGGAAGAGTTTAATCTCCACCTCACAGGTGACATCCATGCCATCACTGTATCTAATAACCTTGTT
GCTGCGGCTATTGATGCTCAGCTATTTCATGAACTGACCCAGACAGACAAGGCTATCTTTACTCATTTGGTGCCATCAGT
AAATGGAGTGAGAAAGTTCTCTGATATCCACATACAAAGGTTAAACAGACTAGGCATTGACAAGACTGACTCTACCACAC
TGACAGATGAAGAGATAAACAGATTTGCAAGATTGGACATTGATCCAGAAACCATAGCTTGGCAAAGAGTGTTGAATACC
AATGATAGATTCCTGAGGAAGATCACGATTGGACAGGCTCCAACGAAGAAAAGTCACACACAGACGGTCCACTTTGATAT
CTCTGTGGCCAGTGAAATTATGGCTGTCCTGGCTCTCACCACTTCTCTAGAAGACAGGAGAGAGAGACTGGGCAAAATGG
TGGTGGCATCCAGTAAGAAAGGAGAGCCCGTCAGTGCTGAAGATCTGGGGGTGAGTGGTGCATTGATAGTGCTTATGAAG
GACACAATCAAGCCCAATCTCATGCAGAGATTGGAGGGCACTCCAGTGTTTGTCCATGCAGGCCCATTTGCCAACATCAC
ACACGGCAATTCCTCTATCATTGCAGACCGGATCACACTCTAGCTTGTTGGCCCAGAAGGGTTTGTAGTGACGGAGGCGG
GATTTGGAGCAGACATTGGAATAGAAAAGTTTTTTAACATCAAATCCCAGTATTCTGGTCTCCACCCTCACGTGGTGGTG
CTTGTTGCCACTGTCAGCGCTCTAAAGATGCACAGGGGTGGCCCTATGGTCACTGCTGGAATGCCTCTTCCCAAGGCTTA
CATAGAGGAGAACCTGGAGCTGGTTGAAAAAGGCTTCAGTAACTTGAAGAAACAAACTGAAAATGCCAGAATGTTTGGAA
TTCCAGTAGTAGTGGCCGTGAATGCATTCAAGACAGATACAGAGACTGAGCTGGACCTCATCGGCTGCCTTTCCAGAGAA
CAGAGGGCTTTTGATGCCGTGAAGTGCACTCACTGGCAGAAGGGGGCAAGGGTACCTTAGCCCTGGCTCAGGCTGTCCAG
AGAGCAGGACAAGCACCCAGCAGCTTCCAACTCCTTTATGACCTCAAGCTCCCAGTTGAGGATAAAATCAGGATCATTGC
ACAGAAGATCTATGGAGCAGACAACATTGAATCACTCCTCAAAGCTCAACACAAAGCTGAAGTCTACACAAAGCAGGGCT
TTGGGAATCTCCCCATCTGCATGGCCAAAACACACTTGTCCTTGTCTCACAACCCAGAGCGAAAAGGTGTCCCTACAGGA
TTCTTTCTGCCCATTCGCGACATCCATGCCAGCATCGGGGCTGGTTTTCTGTACCCTTTAGTAGGAACGATGAGC

Alignment

ORF - retro_ptro_3223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.08 %
• Parental protein coverage: 65.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVPGGVGPMTVAMLMQSTVESAKRFLEKFKPGKWMIQYNNLNLKTPVPSDIDISRSCKPKPIGKLAREIG
          PVPGG.G.MTVAMLMQSTVESAK.FLEKFKPGKWMIQYNNLNLKTPV.SDIDISRSCKPKPIGKLA..IG
Retrocopy PVPGGLGLMTVAMLMQSTVESAKLFLEKFKPGKWMIQYNNLNLKTPVRSDIDISRSCKPKPIGKLA*GIG

Parental  LLSEEVELYGETKAKVLLSALERLKHRPDGKYVV-VTGITPTPLGEGKSTTTIGLVQALGAHLYQNVFAC
          LLSEEVELYGETKAKVLLSALERLKH.PDGKY.V.VT.ITPTPLGEGKSTTTIGLVQAL.AHL.QN.F.C
Retrocopy LLSEEVELYGETKAKVLLSALERLKHQPDGKYQV<VT*ITPTPLGEGKSTTTIGLVQALLAHLSQNFFMC

Parental  VRQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDARIFHELTQTDKALFNR
          VRQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAIT..NNLVAAAIDA..FHELTQTDKA.F..
Retrocopy VRQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITVSNNLVAAAIDAQLFHELTQTDKAIFTH

Parental  LVPSVDGVRRFSDIQIRRLKRLGIEKTDPTTLTDEEINRFARLDIDPETITWQRVLDTNDRFLRKITIGQ
          LVPSV.GVR.FSDI.I.RL.RLGI.KTD.TTLTDEEINRFARLDIDPETI.WQRVL.TNDRFLRKITIGQ
Retrocopy LVPSVNGVRKFSDIHIQRLNRLGIDKTDSTTLTDEEINRFARLDIDPETIAWQRVLNTNDRFLRKITIGQ

Parental  APTEKGHTRTAQFDISVASEIMAVLALTTSLEDMRERLGKMVVASSKKGEPVSAEDLGVSGALTVLMKDA
          APT.K.HT.T..FDISVASEIMAVLALTTSLED.RERLGKMVVASSKKGEPVSAEDLGVSGAL.VLMKD.
Retrocopy APTKKSHTQTVHFDISVASEIMAVLALTTSLEDRRERLGKMVVASSKKGEPVSAEDLGVSGALIVLMKDT

Parental  IKPNLMQTLEGTPVFVHAGPFANIAHGNSSIIADRIALKLVGPEGFVVTEAGFGADIGMEKFFNIKCRYS
          IKPNLMQ.LEGTPVFVHAGPFANI.HGNSSIIADRI.L.LVGPEGFVVTEAGFGADIG.EKFFNIK..YS
Retrocopy IKPNLMQRLEGTPVFVHAGPFANITHGNSSIIADRITL*LVGPEGFVVTEAGFGADIGIEKFFNIKSQYS

Parental  GLCPHVVVLVATVRALKMHGGGPTVTAGLPLPKAYIQENLELVEKGFSNLKKQIENARMFGIPVVVAVNA
          GL.PHVVVLVATV.ALKMH.GGP.VTAG.PLPKAYI.ENLELVEKGFSNLKKQ.ENARMFGIPVVVAVNA
Retrocopy GLHPHVVVLVATVSALKMHRGGPMVTAGMPLPKAYIEENLELVEKGFSNLKKQTENARMFGIPVVVAVNA

Parental  FKTDTESELDLISRLSREHGAFDAVKCTHW-AEGGKGALALAQAVQRAAQAPSSFQLLYDLKLPVEDKIR
          FKTDTE.ELDLI..LSRE..AFDAVKCTHW.AEGGKG.LALAQAVQRA.QAPSSFQLLYDLKLPVEDKIR
Retrocopy FKTDTETELDLIGCLSREQRAFDAVKCTHW<AEGGKGTLALAQAVQRAGQAPSSFQLLYDLKLPVEDKIR

Parental  IIAQKIYGADDIELLPEAQHKAEVYTKQGFGNLPICMAKTHLSLSHNPEQKGVPTGFILPIRDIRASVGA
          IIAQKIYGAD.IE.L..AQHKAEVYTKQGFGNLPICMAKTHLSLSHNPE.KGVPTGF.LPIRDI.AS.GA
Retrocopy IIAQKIYGADNIESLLKAQHKAEVYTKQGFGNLPICMAKTHLSLSHNPERKGVPTGFFLPIRDIHASIGA

Parental  GFLYPLVGTIT
          GFLYPLVGT..
Retrocopy GFLYPLVGTMS

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	33.75 RPM
SRP007412_cerebellum	0.00 RPM	33.63 RPM
SRP007412_heart	0.03 RPM	45.06 RPM
SRP007412_kidney	0.05 RPM	147.16 RPM
SRP007412_liver	0.20 RPM	288.72 RPM
SRP007412_testis	0.00 RPM	10.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3223 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3223 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4839
Gorilla gorilla	retro_ggor_3018

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015967	1 retrocopy	retro_cfam_300,
Homo sapiens	ENSG00000100714	1 retrocopy	retro_hsap_4839,
Gorilla gorilla	ENSGGOG00000005251	1 retrocopy	retro_ggor_3018,
Microcebus murinus	ENSMICG00000013011	6 retrocopies	retro_mmur_1069, retro_mmur_1250, retro_mmur_1462, retro_mmur_451, retro_mmur_777, retro_mmur_993,
Macaca mulatta	ENSMMUG00000001319	1 retrocopy	retro_mmul_2583,
Pan troglodytes	ENSPTRG00000006435	1 retrocopy	retro_ptro_3223 ,