Kidney - Loop of Henle Cocuration: Difference between revisions
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Revision as of 06:17, 8 October 2009
- Participants
- Dr. Yasmin Alam-Faruque - EBI. email: yalam@ebi.ac.uk
- Dr. Rebecca Foulger - EBI. email: rfoulger@ebi.ac.uk
- Dr. Fiona McCarthy - AgBase. email: FMcCarthy@cvm.msstate.edu
- Genes of interest to start annotating
This table represents a GO annotation starting list for this project showing the UPKB accession number for each gene and an approximate number of papers from a quick pubmed search for the gene name and the species and kidney function. Please feel free to start annotation whenever suits you and to add comments for discussion and completion date etc. If you come across further genes of interest please send them to me so that I can update the list.
Involvement in kidney function | Mouse | Human | Rat | Chicken | Xenopus Laevis | Xenopus tropicalis | Completed | Comments* | |
---|---|---|---|---|---|---|---|---|---|
Tesc | Q9JKL5/ 1 | Q96BS2/ 1 | IPI00769039/ - | A0AVX7/ 1 | Q5U554/ 1 | Q0V9B1/ - | PMID 19345287 state (pg 278, top right) that a lack of kidney expression by immunocytochemistry in mice embryos suggests that TESC might not have a significant role in kidney[RF].
PMID 11145610 states that TESC mRNA was present in mouse fetal testis restricted to the testicular cords but was not expressed in the ovary or metanephros. Col9a3 was present at low levels in female and male gonads at 11.5 days and thereafter upregulated in male gonads only and expression was restricted to testicular cords; Renin was localized in cells of the interstitium and cells at the border between the gonad and mesonephros (from abstract and Fig.6 A-L ISH) [YAF 26/08/09] | ||
Slc23a1 | Q9Z2J0/ 3 | Q9UHI7/ 7 | Q9WTW7/ 4 | B9VMA9 (Slc23a2)/ 1 | -/ 1 | B0JZG0 (Slc23a2)/ - | There's no chicken or Xenopus Slc23a1 TrEMBLs yet: Slc23a2 entries are closest match, tho according to PMID 17689499, Slc23a1 (SVCT1) is expressed in epithelial systems (eg kidney), whereas Slc23a2(SVCT2) is more expressed in metabolic tissues (eg pancreas, brain, adrenals)[RF].
PMID 17258485 demonstrates presence of chicken-specific SVCT1 mRNA (via RT-PCR)in both cultured and native proximal tubule cells using primers derived from chicken ESTs and hence demonstrates vitamin C transport [YAF 28/08/09] | ||
Ctnnb1 | Q02248/ 49 | P35222/ 84 | Q9WU82/ 15 | O42486/ 1 | P26233/ 4 | Q28GC2/ - | |||
Lamb1-1 | P02469/ 1 | P07942/ 1 | P15800(Lamb2)/ - | O57484/ - | Q5XHI6/ - | B3DLV1/ - | |||
Egr1 | P08046/ 3 | P18146/ 9 | P08154/ 6 | O73691/ - | Q6GQH4/ - | A4II20/ - | |||
Pou3f3 (Brn1) | P31361/ 3 | P20264/ 2 | Q63262/ - | Q52HB4/O73861/ - | P70030 (pou3f2-B)/ - | A1L0Z1 (Pou3f4)/ - | PMID 12925600 shows that Brn1 is essential for kidney nephron development and function [YAF 18/09/09] | ||
Id2 | P41136/ 4 | Q02363/ 1 | P41137/ 1 | O73933/ - | Q9YGL0/ - | Q6PBD7/ - | |||
Cdh11 | P55288/ 3 | P55287/ 1 | Q9JIW2/ 1 | O93319/ - | O93264/ - | Q5EAM2/ - | |||
Aldh1l1 | Q8R0Y6/ - | O75891/ - | P28037/ - | O93344/ - | Q6GNL7/ - | Q63ZT8/ - | |||
Tfap2b | Q61313/ 3 | Q92481/ 3 | P58197/ - | O93346/ - | Q66J14/ - | Q28C75/ - | |||
Ttr | P07309/ 1 | P02766/ 4 | P02767/ - | P27731/ 1 | Q9W649/ 3 | A4QNN7/ - | |||
Ptn | P63089/ 2 | P21246/ 1 | P63090/ 3 | P32760/ - | P48532/ - | A4IH83/ - | |||
Ccnd1 | P25322/ 21 | P24385/ 24 | P39948/ 15 | P55169/ - | P50755/ - | Q6GLD3/ - | |||
Irx3 | P81067/ 2 | P78415/ - | - | Q9PUR3/ - | O42261/ 1 | Q6NVN3/ - | comparitive paper PMID 17875669 looking at expression of Irx1, 2 and 3 in the mouse LOH (pg 2361-2362) and the function of Xenopus irx3 in the pronephron:
Expression patterns for Xenopus and mouse (PMID 17875669) suggest a function for Irx3 in patterning the nephron by specifying pronephron intermediate tubule and metanephron Henle's loop fates respectively. The function in frogs is confirmed with knock-outs [RF, 15/09/09]. PMID 18715948 looks at Irx1 and Irx2 in Xenopus pronephros development. . | ||
Irx2 | P81066/ 1 | Q9BZI1/ - | - | Q9PU52/ - | Q6DCQ1/ - | Q66IK1/ - | " Need to be slightly cautious about nomenclature for the irx proteins. Human irx3 is called irx1 in some submissions, and mouse irx2 is called irx6 in PMID 10704856, for example. [REF 24/09/09] | ||
Irx1 | P81068/ 2 | P78414/ - | - | Q9I9C5/ - | Q9YGK8/ 1 | Q6F2E3/ - | "
PMID 17875669 show Xirx1 is dispensable for kidney development, but PMID 18715948 show Xirx1 and Xirx3 are required early on to maintain kidney field identity, and then later for formation of the intermediate tubule (contained in the LOH in mammals) [REF 25/09/09] | ||
Pax2 | P32114/ 40 | Q02962/ 34 | IPI00364303/ 4 | Q9PTX1/ 3 | O57685+O57682/ - | Q28IR6/ - | |||
Pax8 | Q00288/ 23 | Q06710/ 22 | P51974/ 1 | -/ 2 | Q9PUK5/ 1 | A0JMA6/ - |
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2: Weavers H, Prieto-Sánchez S, Grawe F, Garcia-López A, Artero R, Wilsch-Bräuninger M, Ruiz-Gómez M, Skaer H, Denholm B. The insect nephrocyte is a podocyte-like cell with a filtration slit diaphragm. Nature. 2009 Jan 15;457(7227):322-6. Epub 2008 Oct 29. PMID 18971929. 3: Zhuang S, Shao H, Guo F, Trimble R, Pearce E, Abmayr SM. Sns and Kirre, the Drosophila orthologs of Nephrin and Neph1, direct adhesion, fusion and formation of a slit diaphragm-like structure in insect nephrocytes. Development. 2009 Jul;136(14):2335-44. Epub 2009 Jun 10. PMID 19515699.
1. NTR item #2846310: to request a new term 'sodium-dependent L-ascorbic acid transmembrane transporter activity' as mentioned in PMID 10631088 (IDA) for the function of SVCT1/SLC23A1 (Q9UHI7). I'm not sure if it would be a child of either GO:0022857 transmembrane transporter activity or of GO:0008523 sodium-dependent multivitamin transmembrane transporter activity? I also think perhaps that there should be another new term 'L-ascorbic acid transmembrane transporter activity' as a child of GO:0022857 transmembrane transporter activity and GO:0015229 L-ascorbic acid transporter activity and then the term 'sodium-dependent L-ascorbic acid transmembrane transporter activity' could be a child of that (too)? - Midori added: sodium-dependent L-ascorbate transmembrane transporter activity GO:0070890 [YAF 01/09/09] 2. NTR item #2849019: to request new term transepithelial ascorbic acid transport (or transepithelial ascorbate transport) , as a child of GO:0070633 transepithelial transport, for annotation of the SVCT1 and SVCT2 proteins as described in the recent publication PMID 18417304. -Midori added transepithelial L-ascorbic acid transport GO:0070904 [YAF 03/09/09]
Added SourceForge request: #2859892 for 2 new kidney terms: specification of kidney anlage ; GO:NEW, maintenance of kidney anlage identity ; GO:NEW Needed for annotation of PMID 17875669 [REF 16/09/09] Added SourceForge request: #2860000 for 6 new terms relating to the proximal/distal subdivision of the nephron late in kidney development:
[REF 16/09/09]
From PMID 12925600 - IMP studies show that Brn1 is essential for the development and function of the kidney nephron. will need to request new terms (possibly the same as the above 'specification of .....' terms requested by Becky or maybe children of the above? (will need to discuss with Becky)): ie:
From PMID 11997177 for P19091 (ANDR_MOUSE) -needed NTR for POU domain binding as a child of GO:0019904 protein domain specific binding. This is required for annotation of the binding of Androgen receptor protein to the POU domains of Brn1 and Oct1 proteins in PMID:11997177. 'POU domain binding'- GO NEW possible definition: "Interacting selectively and non-covalently with a POU domain of a protein, In eukaryotes, the POU proteins are usually transcription factors" SF#2871338 (YAF 01/10/09). Midori added POU domain binding GO:0070974.
Yasmin Alam-Faruque and Emily Dimmer.
1. Janech, MG, Raymond JR, Arthur JM (2007); Proteomics in renal research; Am J Pysiol Renal Physiol; 292(2), F501-12 (PMID 17107941). 2. Halperin ML, Kamel KS, Oh MS (2008), Mechanisms to concentrate the urine: an opinion. Curr Opin Nephrol Hypertens; 17(4), 416-22 (PMID 18660679). 3. Khan KN, Stanfield KM et al; (2001); Cylooxygenase-2-expression in the developing human kidney Pediatr Dev Path 4(4) 461-6 (PMID 11779048). 4. Chan T, Asashima M (2006) Growing kidney in the Frog; Nephron Exp Nephrol; 103, e81-85 (PMID 16554664). 5. Gill PS, Wilcox CS (2006); NADPH oxidases in the kidney; Antioxid Redox Signal 8(9-10), 1597-607 (PMID 16987014). 6. Jones EA (2005); Xenopus: a prince among models for pronephric kidney development; J Am Soc Nephrol 16(2), 313-21 (PMID 15647339). 7. Gambaryan SP (1992); Development of the metanephros in the chick: maturation of glomerular size and nephron length; Anat Embryol (Berl); 185(3):291-7. (PMID 1575329). 8. Lerner J (1984) Cell membrane amino acid transport processes in the domestic fowl (Gallus domesticus). Comp Biochem Physiol A Comp Physiol; 78(2):205-15. (PMID 6146442). 9. Gagnon E, Forbush B, Caron L, Isenring P.(2003) Functional comparison of renal Na-K-Cl cotransporters between distant species. Am J Physiol Cell Physiol.284(2):C365-70. (PMID 12388059). 10. Bankir, L., and de Rouffignac, C. (1985) Urinary concentrating ability : insights from comparative anatomy. Am. J. Physiol. Regulatory Integrative Comp. Physiol. 249: p.643-666. (PMID 3934988) 11. Dihazi H., Rahman, AA., Agarwal, NK, Doncheva, Y., Muller, GA. (2005) Proteomics analysis of cellular response to osmotic stress in TALH-cells. Mol. Cell Proteomics 4: 1445-1458.(PMID 15975915) [[Link title]] Yasmin Alam-Faruque 13:27, 18 August 2009 (UTC) |