RetrogeneDB ID: retro_pabe_3763

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:57901598..57903573(-)
• Located in intron of: ENSPPYG00000020406

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD1L
• Ensembl ID: ENSPPYG00000017105
• Aliases: None
• Description: methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like [Source:HGNC Symbol;Acc:21055]

Sequence

>retro_pabe_3763
GGTGGCTTAGGGCTCATGATGGTTGCAATGCTCATGCAGAGCACAGTAGAGAGTGCCAAGCGTTTCCTGGAGAAATTTAA
GCCAGGAAAGTGGATGATTCAGTATAACAACCTTAACCTCAAGACACCGGTTCCAAGTGATATTGATGTATCATGATCTT
GTAAACCGAAGCCCATTGGTAAGCTGGCTTGAGAAATTGGTCTGCTGTCTGAAGAGGTAGAATTATATGGTGAAACAAAG
GCCAAAGTTCTGCTGTCAGCACTAGAACACCTGAAGCACCAGCCTGATGGGAAATATCAGGTGGTGACTGGAATAACTCC
AACACCCCTGGGAGAAGGGAAAAGCACGACTACAATCAGACTGGTGCAAGCCCTTCTTGCCCATCTCTACCAGAATATGT
GTGTGCGACAGCCTTCTCAGGGCCCCACCTTTGGAATAAAAGGTGGTGCTGCAGAAGGCAGCTACTCCCAGGTCATTCCT
ATGGAAGAGTTTAATCTCCACCTCACAGGTGACATCCATGCCATCACTGTATCTAATAACCTTGTTGCTGCGGCCATTGA
TGCTCAGATATTTCATGAACTGACCCAGACAGACAAGGCTATCTTTAATCATTTGGTGCCATCAGTAAATGGAGTGAGAA
AGTTCTCTGATATCCACATACAAAGGTTAAACAGACTAGGCATTAACAAGACTGACTCTACCACACTGACAGATGAAGAG
ATAAACAGATTTGCAAGATTGGACATTGATCCAGAAACCATAGCTTGGCAAAGAGTGTTGGATACCAATGATAGATTCCT
GAGGAAGATCATGATCGGACAGGCTCCAACGAAGAAAAGTCACACACAGACGGCCCAGTTTGACATCTCTGTGGCCAGTG
AAATTATGGCTGTCCTGGCTCTCACCACTTCTCTAGAAGACAGGAGAGAGAGACTGGGCAAAATGGTGGTGGCATCCAGT
AAAAAAGGAGAGCCCGTCAGCGCTGAAGGTCTGGGGTGAGTGGTGCATTGATAGTGCTTATGAAGGACACAATCAAGCCC
AATCTCATGCAGACATTGGAGGGCACTCCAGTGTTTGTCCATGCCGGCCCGTTTGCCAACATCACACATGGCAATTCCTC
TATCATTGCAGACCGGATCACACTCTAGCTTGTTGGCCCAGAAGGGTTTGTAGTGACGGAAGCGGGATTTAGAGCAGACA
TTGGAATAGAAAAGTTTTTTAACATCAAATCCCGGTATTCCAGCCTCTGCCCTCACGTGGTGGTGCTTGTTGCCACTGTC
AGCACTCTAAAGATGCACAGGGGCCCCTATGGTCACTGCTGGAATGCCTCTTCCCAAGGCTTACATAGAGGAGAACCTGG
GGCTGGTTGAAAAAGGCTTCAGTAACTTGAAGAAACAAATTGAAAATGCCAGAATGTTTGCAATTCCAGTAGTAGTGGCC
GTGAATGCATTCAAGATGAATACAGAGACTGAGCTGGACCTCATCAGCTGCCTTTCCAGAGAACATAGGGCTTTTGATGC
CGTGAAATGCACTCACTGGGCAGAAGGGGGCAAGGCTACCTTAGCCCTGGCTCAGGCTGTCCAGAGAGCAGGACAAGCAC
CCAGCAGCTTCCAACTCTTTTATGACCTCAAGCTCCCAGTTGAGGATAAAATCAGGATCATTGCACAGAAGATCTATGGA
GCAGACAACATTGAATTACTCCTCAAAGCTCAACACAAAGCTGAAGTCTACACAAAGCAGGGCTTTGGGAATCTCCCCAT
CTGCATGGCCAAAACACACTTGTCCTTGTCTCACAACCCAGAGCAAAAAGGTGTCCCTACAGGATTTGTTCTGCCCATCG
CGACATCCATGCCAGCATCGGGGCTGGTTTTCCGTAACCTTTAGTAGGAACGATGAGCACAATGGACTCCCCACCCAGCC
CTGTTTTTATGATACTGATTTGGACCCTGAAACAGAACAGGTGAATGGATTATTC

Alignment

ORF - retro_pabe_3763 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.17 %
• Parental protein coverage: 67.79 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GDVILLAAALRIQNMVSSGRRWLREQQHRRWRLHCLKLQPLSPVPSDIEISRGQTPKAVDVLAKEIGLLA
          G...L...A...Q..V.S..R.L.......W......L....PVPSDI..S....PK....LA.EIGLL.
Retrocopy GGLGLMMVAMLMQSTVESAKRFLEKFKPGKWMIQYNNLNLKTPVPSDIDVS*SCKPKPIGKLA*EIGLLS

Parental  DEIEIYGKSKAKVRLSVLERLKDQADGKYILVAGITPTPLGEGKSTVTIGLVQALTAHLNVNSFACLRQP
          .E.E.YG..KAKV.LS.LE.LK.Q.DGKY..V.GITPTPLGEGKST.TI.LVQAL.AHL..N...C.RQP
Retrocopy EEVELYGETKAKVLLSALEHLKHQPDGKYQVVTGITPTPLGEGKSTTTIRLVQALLAHLYQNM--CVRQP

Parental  SQGPTFGVKGGAAGGGYAQVIPMEEFNLHLTGDIHAITAANNLLAAAIDTRILHENTQTDKALYNRLVPS
          SQGPTFG.KGGAA.G.Y.QVIPMEEFNLHLTGDIHAIT..NNL.AAAID..I.HE.TQTDKA..N.LVPS
Retrocopy SQGPTFGIKGGAAEGSYSQVIPMEEFNLHLTGDIHAITVSNNLVAAAIDAQIFHELTQTDKAIFNHLVPS

Parental  VNGVREFSEIQLPRLKKLGINKTDPSTLTEEEVSKFARLDIDPSTITWQRVLDTNDRFLRKITIGQGNTE
          VNGVR.FS.I...RL..LGINKTD..TLT.EE...FARLDIDP.TI.WQRVLDTNDRFLRKI.IGQ..T.
Retrocopy VNGVRKFSDIHIQRLNRLGINKTDSTTLTDEEINRFARLDIDPETIAWQRVLDTNDRFLRKIMIGQAPTK

Parental  KGYSRQAQFDIAVASEIMAVLALTDSLADMKARLGRMVVASDTSGQPVTADDLG-VTGALTVLMKDAIKP
          K.....AQFDI.VASEIMAVLALT.SL.D...RLG.MVVAS...G.PV.A..LG.V.GAL.VLMKD.IKP
Retrocopy KSHTQTAQFDISVASEIMAVLALTTSLEDRRERLGKMVVASSKKGEPVSAEGLG<VSGALIVLMKDTIKP

Parental  NLMQTLEGTPVFVHAGPFANIAHGNSSVLADKIALKLVGEEGFVVTEAGFGADIGMEKFFNIKCRASGLV
          NLMQTLEGTPVFVHAGPFANI.HGNSS..AD.I.L.LVG.EGFVVTEAGF.ADIG.EKFFNIK.R.S.L.
Retrocopy NLMQTLEGTPVFVHAGPFANITHGNSSIIADRITL*LVGPEGFVVTEAGFRADIGIEKFFNIKSRYSSLC

Parental  PNVVVLVAT-VRALKMHGGGPSVTAGVPLKKEYTEENIQLVADGCCNLQKQIQIAQLFGVPVVVALNVFK
          P..VV.......AL....G.P.VTAG.PL.K.Y.EEN..LV..G..NL.KQI..A..F..PVVVA.N.FK
Retrocopy PH-VVVLVA>LSAL*RCTGAPMVTAGMPLPKAYIEENLGLVEKGFSNLKKQIENARMFAIPVVVAVNAFK

Parental  TDTRAEIDLVCELAKRAGAFDAVPCYHWSVGGKGSVDLARAVREAASKRSRFQFLYDVQLPIVDKIRTIA
          ..T..E.DL...L.....AFDAV.C.HW..GGK....LA.AV..A....S.FQ..YD..LP..DKIR.IA
Retrocopy MNTETELDLISCLSREHRAFDAVKCTHWAEGGKATLALAQAVQRAGQAPSSFQLFYDLKLPVEDKIRIIA

Parental  QAVYGAKDIELSPEAQAKIDRYTQQGFGNLPICMAKTHLSLSHQPDKKGVPRDFILPIS-DVRASIGAGF
          Q..YGA..IEL...AQ.K...YT.QGFGNLPICMAKTHLSLSH.P..KGVP..F.LPI..D..ASIGAGF
Retrocopy QKIYGADNIELLLKAQHKAEVYTKQGFGNLPICMAKTHLSLSHNPEQKGVPTGFVLPIA<DIHASIGAGF

Parental  IYPLVGTMSTMPGLPTRPCF-YDIDLDTETEQVKGLF
          ..PLVGTMSTM...P..P.F.YD.DLD.ETEQV.GLF
Retrocopy P*PLVGTMSTMDS-PPSPVF<YDTDLDPETEQVNGLF

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	1.38 RPM	28.03 RPM
SRP007412_cerebellum	1.22 RPM	39.89 RPM
SRP007412_heart	1.99 RPM	6.35 RPM
SRP007412_kidney	4.51 RPM	9.68 RPM
SRP007412_liver	15.06 RPM	6.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3763 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3763 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3763 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000017105	1 retrocopy	retro_pabe_3763 ,