RetrogeneDB ID: retro_ptro_2162

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:73117672..73118608(+)
• 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_2162
AATGAAGCTGTTGTCAGGAAACTGGCCCAGTGGATCAAGCAGGAAGTGCGGCAGGAGGTGGAGGAGTAGGTGGCCTCTGG
CAACAAAGGGCCATGCCTGAGCGTGGCTCTGGTCAGCAAAACTCCTGCAAGTCACTGCCATATCCTCAACAAAACCAGGG
CAGCTGCAGATGTGGGAATCAACAGTGAGATAATTGTGAAACCAGCTTCAATTTCAGAGGAAGAATTGTTGAATTTAATC
AATAAATTGAATAATGATGGTAATGTAGATGGCCTCCTTCTCCACCTGCCTCTTCCAGAGCACATTGATGAGAGAAAGAT
CTGCAATTCTGTTTTTCCAGATAAGGATGTTGATGGCTTTCATGTAATTAATGTAGGGCGAATGTATCTGGACCAGTATT
CCGTATACCAGCTACTCCATGCAGTGTGTGGGAAATAATTAAGCAAACTGGCATTCCAACCCTAGGGAAGAATGTGGTTG
TGGCTGGAAGGTCAAAAAATGTTGTAATGCCTATTGCAATGTCACTGCACACAGATGGGGTGCATGAACGTCACGGAGGT
GATGCCACTGTTATAATATCTCATTGATATACCCCCAAAGAGCAGTTGAGGAAATACAATTCTTGCAGATATTGTAATAT
CTGTTGCAGGTGTTCCAAATCTGATCACAGCAAATATGACCAAGGAAGAAGCAATAGCATTGATGTGGGAATAGATACAG
TTCAAGATCCTGTAACTGCTAAACCTAAGTTGGTTGGAAATGTGGATTTTAAAGGAGTTAGGCAAAAAGCCAGTTATATC
ACTCCAGTTTCTGGAGGTGTTGGCCCTATGACAGTGGCAATGCTAATGAAGAATACCATAATTGCTGCAAAAAAAAGTGC
TAAGGCTTGAAGAACGGAAAGTGCTGAAGTCTAAAGAGCTTGGAGTAGCCACTAAC

Alignment

ORF - retro_ptro_2162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.75 %
• Parental protein coverage: 90.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  NEAVVISGRKLAQQIKQEVRQEVEEWVASGNKRPHLSVILVGENPASHSYVLNKTRAAAAVGINSETIMK
          NEAVV...RKLAQ.IKQEVRQEVEE.VASGNK.P.LSV.LV...PASH...LNKTRAAA.VGINSE.I.K
Retrocopy NEAVV---RKLAQWIKQEVRQEVEE*VASGNKGPCLSVALVSKTPASHCHILNKTRAAADVGINSEIIVK

Parental  PASISEEELLNLINKLNNDDNVDGLLVQLPLPEHIDERRICNAVSPDKDVDGFHVINVGRMCLDQYSM-L
          PASISEEELLNLINKLNND.NVDGLL..LPLPEHIDER.ICN.V.PDKDVDGFHVINVGRM.LDQYS...
Retrocopy PASISEEELLNLINKLNNDGNVDGLLLHLPLPEHIDERKICNSVFPDKDVDGFHVINVGRMYLDQYSV<I

Parental  PATPWGVWEIIKRTGIPTLGKNVVVAGRSKNVGMPIAMLLHTDGAHERPGGDATVTISHRYT-PKEQLKK
          PATP..VWEIIK.TGIPTLGKNVVVAGRSKNV.MPIAM.LHTDG.HER.GGDATV.ISH.YT.P......
Retrocopy PATPCSVWEIIKQTGIPTLGKNVVVAGRSKNVVMPIAMSLHTDGVHERHGGDATVIISH*YT<PQRAVEE

Parental  -HTILADIVISAAGIPNLITADMIKEGAAV-IDVGINRVHDPVTAKPKLVGDVDFEGVRQKAGYITPVPG
          ..TILADIVIS.AG.PNLITA.M.KE.A...IDVGI..V.DPVTAKPKLVG.VDF.GVRQKA.YITPV.G
Retrocopy <NTILADIVISVAGVPNLITANMTKEEAIA<IDVGIDTVQDPVTAKPKLVGNVDFKGVRQKASYITPVSG

Parental  GVGPMTVAMLMKNTIIA-AKKVLRLEEREVLKSKELGVATN
          GVGPMTVAMLMKNTIIA....VLRLEER.VLKSKELGVATN
Retrocopy GVGPMTVAMLMKNTIIA>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	0.02 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_2162 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2162 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2162 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3309
Pongo abelii	retro_pabe_2729

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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,