RetrogeneDB ID: retro_pabe_2729

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:43055275..43056199(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD2
• Ensembl ID: ENSPPYG00000012283
• Aliases: None
• Description: methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase [Source:HGNC Symbol;Acc:7434]

Sequence

>retro_pabe_2729
AGGAAACTGGCCCAGTGGATCAAGCAGGAAGTGTGGCAGGAGGTGGAGGAGTAGCTGGCCTCTGGCAACAAACGGCCGTG
CCTGAGCGTGGCTCTGGTCAGCAAAACTCCTACAAGTCATTCCCATACCCTCAACAAAACCAGGGCAGCTGCAGATGTGG
GAATCAACAGTGAGACAATTGTGAAACCAGCTTCAATTTCAGAGGAAGAATTGTTGAATTTAATCAATAAATTGAATAAT
GATGGTAATGTAGATGGCCTCCTTCTCCACCTGCCTCTTCCAGAGCACATTGATGAGAGAAAGATCTGCAATTCTGTTTT
TCCAGATAAGGATGTTGATGGCTTTCATGTAATCAATGTAGGGTGAATGTAACTGGACCAGTATTCCATATACCAGCTAC
TCCATGCGGTGTGTGGGAAATAATTAAGCAAACTGGCATTCCAACCCTAGGGAAGAATGTGGTTGTGGCTGGAAGGTCGA
AAAATGTTGTAATGCCCATTGCAATGTCACTGCACACAGATGGGGTGCATGAACGTCACGGAGGTGATGCCACTGTTATA
ATATCTCATTGATATACCCCCAAAGAGCAGTTGACGAAACATACAATTCTTGCAGATATTGTAATATCTGTTGCAGGTGT
TCCAAATCTGATCACAGCAAATATGACCAAGGAAGAAGCAATAGTCATTGATGTGGGAATAGATACAGTTCAAGATCCTG
TAACTGCTAAACCTAAGTTGGTTGGAAATGTGGATTTTAAAGGAGTTAAACAAAAAGCCAGTTATATCACTCCAGTTTCT
GGAGATGTTGGCCCTATGACAGTGGCAATGCTAATGAAGAATACCATAATTGCTGCAAAAAAAAGTGCTGAGGCTTGAAG
AACGGAAAGTGCTGAAGTCTAAAGAGCTTGGAGTAGCCACTAAC

Alignment

ORF - retro_pabe_2729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.94 %
• Parental protein coverage: 88. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKLAQQIKQEVRQEVEEWVASGNKQPHLSVILVGENPASHSYVLNKTRAAADVGINSETIVKPASISEEE
          RKLAQ.IKQEV.QEVEE..ASGNK.P.LSV.LV...P.SHS..LNKTRAAADVGINSETIVKPASISEEE
Retrocopy RKLAQWIKQEVWQEVEE*LASGNKRPCLSVALVSKTPTSHSHTLNKTRAAADVGINSETIVKPASISEEE

Parental  LLNLINKLNNDDNVDGLLVQLPLPEHIDERRICNAVSPDKDVDGFHVINVGRMCLDQYSM-LPATPWGVW
          LLNLINKLNND.NVDGLL..LPLPEHIDER.ICN.V.PDKDVDGFHVINVG.M.LDQYS...PATP.GVW
Retrocopy LLNLINKLNNDGNVDGLLLHLPLPEHIDERKICNSVFPDKDVDGFHVINVG*M*LDQYSI<IPATPCGVW

Parental  EIIKRTGIPTLGKNVVVAGRSKNVGMPIAMLLHTDGAHERPGGDATVTISHRYTPKEQLKKHTILADIVI
          EIIK.TGIPTLGKNVVVAGRSKNV.MPIAM.LHTDG.HER.GGDATV.ISH.YTPKEQL.KHTILADIVI
Retrocopy EIIKQTGIPTLGKNVVVAGRSKNVVMPIAMSLHTDGVHERHGGDATVIISH*YTPKEQLTKHTILADIVI

Parental  SAAGIPNLITADMIKAGAAVIDVGINRVHDPITAKSKLVGDVDFEGVRQKAGYITPVPGGVGPMTVAMLM
          S.AG.PNLITA.M.K..A.VIDVGI..V.DP.TAK.KLVG.VDF.GV.QKA.YITPV.G.VGPMTVAMLM
Retrocopy SVAGVPNLITANMTKEEAIVIDVGIDTVQDPVTAKPKLVGNVDFKGVKQKASYITPVSGDVGPMTVAMLM

Parental  KNTIIA-AKKVLRLEEREVLKSKELGVATN
          KNTIIA....VLRLEER.VLKSKELGVATN
Retrocopy KNTIIA>XXXVLRLEERKVLKSKELGVATN

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	0.06 RPM	2.88 RPM
SRP007412_cerebellum	0.00 RPM	7.17 RPM
SRP007412_heart	0.03 RPM	36.27 RPM
SRP007412_kidney	0.03 RPM	4.18 RPM
SRP007412_liver	0.06 RPM	3.89 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2729 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2729 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3309
Pan troglodytes	retro_ptro_2162

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 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,
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,
Otolemur garnettii	ENSOGAG00000009089	1 retrocopy	retro_ogar_3390,
Pongo abelii	ENSPPYG00000012283	3 retrocopies	retro_pabe_2271, retro_pabe_2729 , retro_pabe_3077,
Pteropus vampyrus	ENSPVAG00000013948	2 retrocopies	retro_pvam_1357, retro_pvam_1414,
Rattus norvegicus	ENSRNOG00000010833	1 retrocopy	retro_rnor_2170,