RetrogeneDB ID: retro_ptro_1846

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:183422962..183423936(+)
• 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_1846
ATGGCTGCGACTTCCCTCATGTCCAGGTTGGCTGCCTGGCTGCTGCAGCCCGTGCACAGCTGCTCCCTCTGCCCTCGCCC
CTTCCACCTCGCGGCAGTTCCAGATGAAGCTGTTGTAATTTCTGGAAGGAAACTGGCCCAGCAGATCAAGCAGGAAGTGC
GGCAGGAGGTAAAAGAGTGGGTGGCCTCAGGCGACAAACGGCCACACCTGAGCATGATCCTGGTTGGCGAGAGTTCTGCA
AGTCACTCCTACGTCCTCAACAAAACCAGGGCAGCTGCAGATGTGGGAATCAACAGTGAGACAATTGTGAAACCAGCTTC
AATTTCAGAGGAAGAATTGTTGAATTTAATCAGCAAACTGAATAATGATGATAATGTAGATGGCCTCCTTGTTCAGCTGC
CTCTTCCAGACATATTGATGAGAGAAGGATCTGCAATGCTGTTTCTCCAGACAAGGATGCTGATGGCTTTCATGTAATTA
ATGCAGGGCGAATGTGTTTGGACCAGTATTCCATGTTACCGGCTACCCCATGCGGTGTGTGAGAAATAATTAAGCGAACT
GACATTCCAACCCTAGGGAAGAATGTGGTTGTGGCTGGAAGGTCAAAAAGTGTTGAAATGCCCATTGCAATGTTACTGCA
CACAGATGGGGCACATGAACGTCCCGGAGGTGATGCCACTGTTACAATATCTTATCGATATACTTCCAAAGAGCAGTTGA
AGAAACATACAATTCTTGCAGATATTGTAATATCTGCTGCAGGTATTCCAAATCTGATCACAGCAGATATGATCAAGGAA
GAAGCAGCAGTCACTGATATGGGAATAAATAGAGTTCATGATCCTGTAACTGCCAAACTGAAGTTGGTTGGAGATGTGGA
TTTTGAAGGAGTCAGACAAAAAGCCGGTTATATCACTCCAGTTCCTGGAGGTGTTGGCCCCATGACAGTGGCAATGCTAA
TGAAGAATACCATT

Alignment

ORF - retro_ptro_1846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.8 %
• Parental protein coverage: 92.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAATSLMSALAARLLQPAHSCSLRLRPFHLAAVRNEAVVISGRKLAQQIKQEVRQEVEEWVASGNKRPHL
          MAATSLMS.LAA.LLQP.HSCSL..RPFHLAAV..EAVVISGRKLAQQIKQEVRQEV.EWVASG.KRPHL
Retrocopy MAATSLMSRLAAWLLQPVHSCSLCPRPFHLAAVPDEAVVISGRKLAQQIKQEVRQEVKEWVASGDKRPHL

Parental  SVILVGENPASHSYVLNKTRAAAAVGINSETIMKPASISEEELLNLINKLNNDDNVDGLLVQLPLPE-HI
          S.ILVGE..ASHSYVLNKTRAAA.VGINSETI.KPASISEEELLNLI.KLNNDDNVDGLLVQLPLP..HI
Retrocopy SMILVGESSASHSYVLNKTRAAADVGINSETIVKPASISEEELLNLISKLNNDDNVDGLLVQLPLPD<HI

Parental  DERRICNAVSPDKDVDGFHVINVGRMCLDQYSMLPATPWGVWEIIKRTGIPTLGKNVVVAGRSKNVGMPI
          DERRICNAVSPDKD.DGFHVIN.GRMCLDQYSMLPATP.GV.EIIKRT.IPTLGKNVVVAGRSK.V.MPI
Retrocopy DERRICNAVSPDKDADGFHVINAGRMCLDQYSMLPATPCGV*EIIKRTDIPTLGKNVVVAGRSKSVEMPI

Parental  AMLLHTDGAHERPGGDATVTISHRYTPKEQLKKHTILADIVISAAGIPNLITADMIKEGAAVIDVGINRV
          AMLLHTDGAHERPGGDATVTIS.RYT.KEQLKKHTILADIVISAAGIPNLITADMIKE.AAV.D.GINRV
Retrocopy AMLLHTDGAHERPGGDATVTISYRYTSKEQLKKHTILADIVISAAGIPNLITADMIKEEAAVTDMGINRV

Parental  HDPVTAKPKLVGDVDFEGVRQKAGYITPVPGGVGPMTVAMLMKNTI
          HDPVTAK.KLVGDVDFEGVRQKAGYITPVPGGVGPMTVAMLMKNTI
Retrocopy HDPVTAKLKLVGDVDFEGVRQKAGYITPVPGGVGPMTVAMLMKNTI

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	0.04 RPM	2.57 RPM
SRP007412_cerebellum	0.00 RPM	6.13 RPM
SRP007412_heart	0.06 RPM	13.73 RPM
SRP007412_kidney	0.03 RPM	11.53 RPM
SRP007412_liver	0.03 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_1846 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1846 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1846 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2732
Pongo abelii	retro_pabe_2271

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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,