C-term/N-term annotation is inconsistent

[kimrutherford]

Hi Val.

I've found that there are three ways that fusions are annotated. For implementing pombase/pombase-chado#993 it would be helpful to standardise.

SPAC1782.04/cox24 is like this with "(C-term)" / "(N-term)" after the gene ID:

FT                   /controlled_curation="term=orthologous to S. cerevisiae
FT                   YLR204W (C-term); date=19700101"
FT                   /controlled_curation="term=orthologous to S. cerevisiae
FT                   YNL295W (N-term); date=20120912"

these aren't displayed on the gene pages at the moment.

his2 and his7 has the C-term/N-term in brackets in the qualifier:

his2 / SPBC1711.13:

FT                   /controlled_curation="term=orthologous to S. cerevisiae
FT                   YCL030C; qualifier=YCL030C(C-term); date=19700101"

his7 / SPBC29A3.02c:

FT                   /controlled_curation="term=orthologous to S. cerevisiae
FT                   YCL030C; qualifier=YCL030C(N-term); date=19700101"

In all other cases the C-term/N-term is after a comma in the qualifier:

qualifier=SPAC19B12.13,C-term

[kimrutherford]

In all other cases the C-term/N-term is after a comma in the qualifier: qualifier=SPAC19B12.13,C-term

I've just noticed that some have an underscore and some have a "-".

[kimrutherford]

There are some that are missing the gene name in the qualifier:

 SPAC13F5.04c  │ VTA1      │ cerevisiae │ N_term
 SPBC3H7.11    │ ABP140    │ cerevisiae │ N_term
 SPAC22E12.10c │ COX15     │ sapiens    │ N-term
 SPBC21C3.07c  │ ABP140    │ cerevisiae │ C_term

"HGMP" looks like a typo here:

 SPBC405.01    │ GART      │ sapiens    │ HGMP:GART,N-term
 SPCC569.08c   │ GART      │ sapiens    │ HGMP:GART,C-term

[kimrutherford]

For completeness, here are all the orthologs and qualifiers from the contig files:

pombe	other	species	qualifier
SPBP4H10.15	ACO2	cerevisiae	SPBP4H10.15,N-term
SPBP4H10.15	MRPL49	cerevisiae	SPBP4H10.15,C-term
SPBC530.12c	CAX4	cerevisiae	SPBC530.12c,C-term
SPBC16A3.11	RAD30	cerevisiae	SPBC16A3.11,N-term
SPBC16A3.11	ECO1	cerevisiae	SPBC16A3.11,C-term
SPAC806.02c	CFD1	cerevisiae	SPAC806.02c,N-term
SPAC806.02c	CIA1	cerevisiae	SPAC806.02c,C-term
SPAC6F12.05c	YJR142W	cerevisiae	SPAC6F12.05c,N-term
SPAC6F12.05c	THI80	cerevisiae	SPAC6F12.05c,C-term
SPAC2C4.12c	TPT1	cerevisiae	SPAC2C4.12c,N-term
SPAC2C4.12c	YAE1	cerevisiae	SPAC2C4.12c,C-term
SPAC22E12.10c	COX15	cerevisiae	SPAC22E12.10c,N-term
SPAC22E12.10c	YAH1	cerevisiae	SPAC22E12.10c,C-term
SPAC22A12.08c	YKR070W	cerevisiae	SPAC22A12.08c,N_term
SPAC22A12.08c	CRD1	cerevisiae	SPAC22A12.08c,C_term
SPAC19B12.13	RSM22	cerevisiae	SPAC19B12.13,N-term
SPAC19B12.13	COX11	cerevisiae	SPAC19B12.13,C-term
SPAC15E1.04	CDC21	cerevisiae	SPAC15E1.04,C-term
SPAC1420.04c	RSM22	cerevisiae	SPAC1420.04c,N-term
SPAC1420.04c	COX11	cerevisiae	SPAC1420.04c,C-term
SPAC13F5.04c	VTA1	cerevisiae	N_term
SPBC3H7.11	ABP140	cerevisiae	N_term
SPBC21C3.07c	ABP140	cerevisiae	C_term
SPBC530.12c	PPT1	sapiens	SPBC530.12c,N-term
SPAC806.02c	NUBP2	sapiens	SPAC806.02c,N-term
SPAC806.02c	CIAO1	sapiens	SPAC806.02c,C-term
SPAC22E12.10c	COX15	sapiens	N-term
SPBC405.01	GART	sapiens	HGMP:GART,N-term
SPCC569.08c	GART	sapiens	HGMP:GART,C-term

[ValWood]

from https://github.com/pombase/curation/issues/3455

At the same time, some of the fusions do not have their human orthologs. Do these too

Annotate human orthologs similarly to S. cerevisiaie (N-ter, C-Term)

Systematic ID Gene name Product description SPAC22A12.08c crd1 cardiolipin synthase/ hydrolase fusion protein Crd1 SPAC806.02c CIA machinery CIA1/CFD1 fusion protein SPAC1420.04c cox1101 cytochrome c oxidase assembly protein Cox1101/ mitochondrial ribosomal protein Rsm22 fusion protein SPAC19B12.13 cox1102 cytochrome c oxidase assembly protein Cox1102/ mitochondrial ribosomal protein Rsm2202, fusion protein SPCC1223.08c dfr1 dihydrofolate reductase/ lysophospholipase fusion protein Dfr1 SPAC22E12.10c etp1 mitochondrial [2Fe-2S] cluster assembly ferredoxin Etp1/ cytochrome oxidase cofactor Cox15, fusion protein SPAC1782.04 cox24 mitochondrial mRNA processing protein Cox24/Pet20 SPBP4H10.15 aco2 mitochondrial ribosomal protein subunit L21/aconitate hydratase, fusion protein SPBC2D10.09 snr1 mitochondrial ribosomal protein subunit S47/3-hydroxyisobutyryl-CoA hydrolase Snr1 SPBC16A3.11 eso1 mitotic cohesin N-acetyltransferase/DNA polymerase eta Eso1 fusion protein SPBC530.12c pdf1 palmitoyl protein thioesterase/ dolichol pyrophosphate phosphatase fusion protein Pdf1 SPCC1450.15 pig-F/3-ketosphinganine reductase fusion protein SPAC6F12.05c tnr3 thiamine diphosphokinase Tnr3/ Nudix hydrolase fusion protein SPAC15E1.04 hal3 thymidylate synthase / phosphopantothenoylcysteine decarboxylase / protein phosphatase inhibitor moonlighting protein Hal3 SPBC13E7.02 cwf24 ubiquitin-protein ligase E3/GCN5-related N acetyltransferase fusion protein SPCC1442.07c wss2 ubiquitin/metalloprotease fusion protein Udp7

METTL17 for cox11 https://www.biorxiv.org/content/10.1101/2022.11.24.517765v1

[ValWood]

reviewed and added missing human to match the S. cerevisiae, and a couple of small fixes to the cerevisiae ones

uniquename uniquename qualifier reference date

SPAC1420.04c COX11 SPAC19B12.13,C-term 2024-08-29 SPAC1420.04c METTL17 SPAC19B12.13,N-term 2024-08-29 SPAC19B12.13 COX11 SPAC19B12.13,C-term 2024-08-29 SPAC19B12.13 METTL17 SPAC19B12.13,N-term 2024-08-29 SPAC22A12.08c HDHD5 SPAC22A12.08c,N-term 2024-08-29 SPAC22A12.08c CRLS1 SPAC22A12.08c,C-term 2024-08-29 SPAC22E12.10c FDX2 SPAC22E12.10c,C-term 2024-08-29 SPAC2C4.12c TRPT1 SPAC2C4.12c,N-term 2024-08-29 SPAC2C4.12c YEA1 SPAC2C4.12c,C-term 2024-08-29
SPAC6F12.05c TPK1 SPAC6F12.05c,C-term 2024-08-29 SPAC6F12.05c NUDT19 SPAC6F12.05c,N-term 2024-08-29 SPBC16A3.11 ESCO1 SPBC16A3.11,C-term 2024-08-29
SPBC16A3.11 POLH SPBC16A3.11,N-term 2024-08-29
SPBC530.12c DOLPP1 SPBC530.12c,C-term 2024-08-29 SPBP4H10.15 ACO2 SPBP4H10.15,C-term 2024-08-29

[ValWood]

So happy to do this it's been on my mind since before you went back to New Zealand. I think I'll treat my self to a glass of wine for this one......much easier in the flat file!