RetrogeneDB ID: retro_cjac_1764

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:18316903..18317766(+)
• Located in intron of: ENSCJAG00000018862

Retrocopy information

• Ensembl ID: ENSCJAG00000018920
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTHFD2L
• Ensembl ID: ENSCJAG00000013883
• Aliases: None
• Description: Probable bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase 2 NAD-dependent methylenetetrahydrofolate dehydrogenase Methenyltetrahydrofolate cyclohydrolase [Source:UniProtKB/Swiss-Prot;Acc:F6ZFR0]

Sequence

>retro_cjac_1764
TTCCACCTCGTGGCAGTTCGAAATGAAGCCGTGGTCATTTCTGGAAGGAAACTGACCCAGCAGATCAAGCAGGAAGGGCA
GCAGGAGATGGAAGAGTGGGTGGCCTCAGGCAATAAGTGGCCACAACTTAGCGTGATCCTCTTTGCCGAGCATCCTGCAA
GTCACTGCTATGTCCTCAACAAAACCAGGGCAGCTGCAGGTATGGGAATCAACAGTGAGACAGTTGTGAAACCGGCTCCA
ATTTCAGAGGAAGAATTGTTGAATTTAATGAATAAACTGAATAATGATGATAACGTAGATGGCCTCCTTGTTCAGCCGGC
TCTTCCAGAGCATATTGATGAGAGAAAGATCTGCAATGCCATTTCTCCAGACAAGGACGTTGATGGCTTTCATGTAATTA
ATGTAGGGCGAATGTGTTTGGACCAGTATTCCATGTTACTGGCTACCCCGCGGGGTGTGGGGAAAATAATTAAGCGAACT
GGCATTCCAACCCTAGGGAAGAATGTGGTTGTGGCTGGAAGGTCAAAAAATGTAGGAATGCCCAGTGCAATGTTACTGCA
CACAGGGCACATGAACGTCCCGGAGGTGATGCCACTGTCACAACATCTCATCGATATACTTCCAAAGAACAGTTGAAGAA
ACATATAATTCTTGCAGATATTGTAATATCTGCTGCAGGCATTCCAAATCTGATCACAGCAGATATGATCAAGGAAGGAG
CAGCAGTTATTGATGTGGGAATAAATAGAGTTCACAATCCCATAACTGCCAAACCCAAGTTGGTTGGAGATGTGGATTTT
GAAGGAGTCAGACAAAAAGCCAGTTCTATCACTCCAGTTCCTGGAGGGCTTGTCCCCATGAGT

Alignment

ORF - retro_cjac_1764 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.41 %
• Parental protein coverage: 83.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FRSSGVRHEAVIISGTEMAKHIQKEIKQGVESWISLGNRRPHLSIILVGDNPASHTYVRNKIRAASAVGI
          F....VR.EAV.ISG......I..E..Q..E.W...GN..P.LS.IL....PASH.YV.NK.RAA...GI
Retrocopy FHLVAVRNEAVVISGRKLTQQIKQEGQQEMEEWVASGNKWPQLSVILFAEHPASHCYVLNKTRAAAGMGI

Parental  CSELILKPKDVSQEELLDITDQLNMDPRVSGILVQLPLPDHVDERMICNGIAPEKDVDGFHIINIGRLCL
          .SE...KP...S.EELL.....LN.D..V.G.LVQ..LP.H.DER.ICN.I.P.KDVDGFH.IN.GR.CL
Retrocopy NSETVVKPAPISEEELLNLMNKLNNDDNVDGLLVQPALPEHIDERKICNAISPDKDVDGFHVINVGRMCL

Parental  DQHSLIPATASAVWEIITRTGIQTFGKNVVVAGRSKNVGMPIAMLLHTDGEHERP-GGDATVTIAHRYTP
          DQ.S...AT...V..II.RTGI.T.GKNVVVAGRSKNVGMP.AMLLHT.G....P.GGDATVT..HRYT.
Retrocopy DQYSMLLATPRGVGKIIKRTGIPTLGKNVVVAGRSKNVGMPSAMLLHT-GHMNVP<GGDATVTTSHRYTS

Parental  KEQLKTHTQLADVIIVAAGIPKLITSDMVKEGAAVIDVGINYVHDPVTGKTKLVGDVDFEAVKKKAGFIT
          KEQLK.H..LAD..I.AAGIP.LIT.DM.KEGAAVIDVGIN.VH.P.T.K.KLVGDVDFE.V..KA..IT
Retrocopy KEQLKKHIILADIVISAAGIPNLITADMIKEGAAVIDVGINRVHNPITAKPKLVGDVDFEGVRQKASSIT

Parental  PVPGGVGPMT
          PVPGG..PM.
Retrocopy PVPGGLVPMS

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
SRP051959_colon	0.20 RPM	1.80 RPM
SRP051959_heart	1.53 RPM	1.28 RPM
SRP051959_kidney	2.09 RPM	1.66 RPM
SRP051959_liver	0.15 RPM	28.94 RPM
SRP051959_lung	1.17 RPM	4.15 RPM
SRP051959_lymph_node	3.40 RPM	0.39 RPM
SRP051959_skeletal_muscle	0.96 RPM	2.29 RPM
SRP051959_spleen	1.13 RPM	1.07 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1764 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1764 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1764 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006627	1 retrocopy	retro_chof_2362,
Callithrix jacchus	ENSCJAG00000013883	1 retrocopy	retro_cjac_1764 ,
Callithrix jacchus	ENSCJAG00000017810	3 retrocopies	retro_cjac_2225, retro_cjac_2568, retro_cjac_3078,
Tupaia belangeri	ENSTBEG00000009980	4 retrocopies	retro_tbel_2436, retro_tbel_2590, retro_tbel_3051, retro_tbel_850,
Tursiops truncatus	ENSTTRG00000002366	1 retrocopy	retro_ttru_397,