AceView offers a comprehensive annotation of human, mouse and nematode genes
reconstructed by co-alignment and clustering of all publicly available
mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable
up-to-date resource on the genes, their functions, alternative variants,
expression, regulation and interactions, in the hope to stimulate
further validating experiments at the bench
This site normally requires a frame enabled viewer,
However, click here to access our full description of gene ZNF90andRPS16P10.
, go to our main page or see our latest news
Homo sapiens complex locus ZNF90andRPS16P10, encoding zinc finger protein 90.
TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
Compact gene diagram
Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron. Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
Read more...
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the
intron and exons table.
Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Proteins supported by a single continuous cDNA sequence lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
Introns are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron.
]^[ A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron).
] ^ ] A blue broken line denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries.
]-[ Pink and
] - ] blue straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Exons: Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal,
blue flags to any single letter variant of the main . More explanations are given in the
gene help file
Expression and GenBank cDNA support
Tissues where expression was observed (from 58 cDNA clones)
Origin of the cDNAs, as reported in GenBank/dbEST (tissue, stage, pathological or normal) shows that the gene is expressed in brain (seen 5 times), neuroblastoma cot 25-normalized (5), head neck (4), neuroblastoma cells (4), ovary (4), neuroblastoma cot 10-normalized (3), pancreas (3), embryonic stem cells, cell lines H1, H7, andh9 (2), embryonic stem cells, dmso-treated H9 cellline (2), epithelioid carcinoma (2), kidney (2), liver and spleen (2), placenta (2), uterus (2), well-differentiated endometrialadenocarcinoma, 7 pooled tumors (2), adenocarcinoma (once), brain, neuroblastoma (once), breast cancer (once), choriocarcinoma (once), embryonic stem cells (once), epithelioid carcinoma cell line (once), human embryonic stem cells (once), hypernephroma (once), kidney, renal carcinoma (ascites) (once), mammary gland (cancer tissue) (once), melanotic melanoma, high MDR (cell line) (once), neuroblastoma, cell line (once), pooled, cerebellum, kidney, placenta,testis, lung, colon, liver, heart, thyroid, bladder,uterus, PCR rescued clones (once), renal cell adenocarcinoma (once), skin (once), stomach (once), thyroid gland (once), tumor, 5 pooled (see description) (once).
58 cDNA clones support the 7 variants of gene ZNF90andRPS16P10
?
This table helps analyze the pattern of expression of the gene, the tissue, cell type or disease state specificity of the alternative variants and to select cDNA clones suitable for your experiments.
cDNA accession Links to the sequence |
Tissue
most 5' clones in red |
Match mRNA |
From bp to bp in mRNA |
From bp to bp in accs. |
Clone encodes complete protein (with AA variation) |
Features |
Anomalies detected by AceView |
Accession match over (% length) |
Base differences relative to genome (% identity) |
NM_007138.1 | | .a | 1 to 3753 | 1 to 3753 | exact | RefSeq, AAA | | 3753/3753 (100 %) | 0 diff (100 %id) |
M61870 | | .a | 28 to 724 | 8 to 706 | | tiling clone, | | 699/706 (99 %) | 6 diff (99.2 %id) |
TI_2016724589 | | .a | 65 to 982 | 240 to 1150 | | | Submitted on the opposite strand | 911/1222 (74 %) | 17 diff (98.7 %id) |
TI_2016724655 | | .a | 65 to 1008 | 236 to 1168 | | | Submitted on the opposite strand | 933/1275 (73 %) | 31 diff (97.6 %id) |
TI_2016724905 | | .a | 65 to 717 | 656 to 5 | | | | 652/1258 (51 %) | 4 diff (99.7 %id) |
TI_2016727149 | | .a | 65 to 621 | 43 to 597 | | | | 555/597 (92 %) | 31 diff (94.9 %id) |
TI_2016730227 | | .a | 65 to 1152 | 38 to 1123 | | | | 1086/1270 (85 %) | 16 diff (98.8 %id) |
TI_2016730519 | | .a | 65 to 1138 | 40 to 1110 | | | | 1071/1247 (85 %) | 21 diff (98.4 %id) |
BC137211 | Pooled, cerebellum, kidney, placenta,testis, lung, colon, liver, heart, thyroid, bladder,uterus, PCR rescued clones | .a | 74 to 2337 | 1 to 2264 | exact | tiling clone, | | 2264/2264 (100 %) | 0 diff (100 %id) |
CN386341 | embryonic stem cells, cell lines H1, H7, andH9 | .a | 74 to 792 | 1 to 719 | | | | 719/719 (100 %) | 0 diff (100 %id) |
BE934091 | head_neck | .b | 1 to 593 | 7 to 598 | | tiling clone, | | 592/598 (98 %) | 8 diff (98.7 %id) |
CV360725 | head_neck | .b | 1 to 462 | 1 to 463 | | tiling clone, | | 463/463 (100 %) | 10 diff (97.9 %id) |
TI_2016724903 | | .b | 444 to 1614 | 1168 to 7 | | tiling clone, | | 1162/1251 (92 %) | 0 diff (100 %id) |
GD136765 | | .b | 657 to 1228 | 700 to 129 | | | Submitted on the opposite strand | 572/703 (81 %) | 0 diff (100 %id) |
TI_2016724751 | | .b | 1062 to 2237 | 1 to 1166 | | | | 1166/1285 (90 %) | 50 diff (96.2 %id) |
AA383761 | thyroid gland | .b | 1084 to 1304 | 1 to 221 | | | | 221/222 (99 %) | 2 diff (99.1 %id) |
TI_2016730079 | | .b | 1090 to 2056 | 30 to 996 | | | | 967/1005 (96 %) | 6 diff (99.5 %id) |
TI_2016724471 | | .b | 1111 to 2241 | 1194 to 70 | | tiling clone, | | 1125/1300 (86 %) | 0 diff (100 %id) |
CX785391 | human embryonic stem cells | .b | 1367 to 2125 | 1 to 759 | | | | 759/760 (99 %) | 1 diff (99.9 %id) |
CD653414 | Embryonic Stem cells | .b | 1581 to 2369 | 7 to 793 | | tiling clone, | | 787/793 (99 %) | 6 diff (99.3 %id) |
N85121 | | .b | 2338 to 2623 | 1 to 283 | | tiling clone, | | 283/283 (100 %) | 5 diff (98.3 %id) |
BF030966 | hypernephroma, Kidney | .b | 2798 to 3448 | 1 to 654 | | tiling clone, | | 654/893 (73 %) | 19 diff (97.9 %id) |
CN357208 | embryonic stem cells, DMSO-treated H9 cellline | .b | 2828 to 3411 | 1 to 584 | | tiling clone, | | 584/586 (99 %) | 1 diff (99.9 %id) |
AI559193 | uterus, well-differentiated endometrialadenocarcinoma, 7 pooled tumors | .b | 3207 to 3657 | 453 to 3 | | | | 451/457 (98 %) | 0 diff (100 %id) |
BX102781 | uterus, well-differentiated endometrialadenocarcinoma, 7 pooled tumors | .b | 3274 to 3657 | 399 to 15 | | AAA | | 385/385 (100 %) | 2 diff (99.5 %id) |
CN357209 | embryonic stem cells, DMSO-treated H9 cellline | .b | 3313 to 3973 | 7 to 666 | | tiling clone, | | 660/666 (99 %) | 7 diff (99.0 %id) |
H13702 | placenta | .b | 3513 to 3652 | 147 to 7 | | | | 141/147 (95 %) | 0 diff (100 %id) |
BF835283.
matches multiple genes | head_neck | .b | 3944 to 4184 | 247 to 6 | | tiling clone, | Submitted on the opposite strand, also hits gene RPS16P1 | 242/249 (97 %) | 1 diff (99.6 %id) |
AW887231 | ovary | .b | 4064 to 4262 | 1 to 197 | | tiling clone, | | 197/200 (98 %) | 5 diff (97.5 %id) |
BG996914 | head_neck | .b | 4090 to 4309 | 1 to 223 | | tiling clone, | | 223/250 (89 %) | 17 diff (93.2 %id) |
CR593334 | Neuroblastoma Cot 25-normalized | .c | 1 to 1918 | 1 to 1918 | exact | tiling clone, | | 1918/1918 (100 %) | 0 diff (100 %id) |
AL523961 | brain, neuroblastoma cells, Neuroblastoma Cot 25-normalized | .c | 1 to 989 | 1 to 978 | F42L D51X M70K | fully sequenced, | | 978/978 (100 %) | 10 diff (99.0 %id) |
DC424219 | | .c | 7 to 743 | 1 to 738 | exact | | | 738/747 (98 %) | 6 diff (99.2 %id) |
BM745333 | stomach | .c | 7 to 134 | 1 to 129 | | | | 129/129 (100 %) | 3 diff (97.7 %id) |
BC004324 | Brain, neuroblastoma | .c | 478 to 1019 | 1 to 540 | | available from MGC, AAA | | 540/540 (100 %) | 29 diff (94.7 %id) |
BC007977 | Kidney, renal carcinoma (ascites) | .c | 493 to 1032 | 1 to 538 | | available from MGC, AAA | | 538/538 (100 %) | 27 diff (95.0 %id) |
BE613031 | adenocarcinoma, ovary | .c | 503 to 1016 | 1 to 511 | | | | 511/511 (100 %) | 29 diff (94.4 %id) |
BG831245 | epithelioid carcinoma cell line, Pancreas | .c | 507 to 1041 | 1 to 541 | | | | 541/783 (69 %) | 28 diff (96.5 %id) |
BG770576 | melanotic melanoma, high MDR (cell line), skin | .c | 508 to 1051 | 1 to 537 | | | | 537/602 (89 %) | 30 diff (95.1 %id) |
BE902767 | choriocarcinoma, placenta | .c | 517 to 982 | 1 to 491 | | | | 491/497 (98 %) | 26 diff (94.8 %id) |
BE908573.
matches multiple genes | epithelioid carcinoma, Pancreas | .c | 528 to 999 | 1 to 481 | | tiling clone, | also hits gene RPS16P1 | 481/1061 (45 %) | 41 diff (96.2 %id) |
BE903974 | epithelioid carcinoma, Pancreas | .c | 704 to 1032 | 202 to 532 | | | | 503/536 (93 %) | 58 diff (89.2 %id) |
BX345385 | Neuroblastoma Cot 25-normalized | .c | 838 to 1779 | 1 to 937 | | | | 937/941 (99 %) | 18 diff (98.1 %id) |
AL562291 | brain, neuroblastoma cells, Neuroblastoma Cot 25-normalized | .c | 959 to 1918 | 963 to 1 | | fully sequenced, | | 963/963 (100 %) | 44 diff (95.5 %id) |
DC427094 | | .c | 1173 to 1932 | 759 to 1 | | tiling clone, | | 759/776 (97 %) | 10 diff (98.8 %id) |
R06858 | liver and spleen | .c | 1223 to 1705 | 1 to 484 | | | | 484/493 (98 %) | 15 diff (97.0 %id) |
AW088912 | ovary, tumor, 5 pooled (see description) | .c | 1754 to 1932 | 190 to 11 | | AAA | | 180/180 (100 %) | 2 diff (98.9 %id) |
DN995268 | breast cancer, Mammary gland (cancer tissue) | .d | 1 to 655 | 8 to 662 | exact | tiling clone, | | 655/662 (98 %) | 6 diff (99.1 %id) |
AK298173 | | .d | 3 to 1203 | 1 to 1201 | | | | 1201/1201 (100 %) | 7 diff (99.5 %id) |
DC360428 | | .d | 3 to 556 | 1 to 553 | | | | 553/553 (100 %) | 6 diff (99.0 %id) |
DC366412 | | .d | 5 to 579 | 1 to 575 | | | | 575/575 (100 %) | 1 diff (99.9 %id) |
CR614976 | Neuroblastoma Cot 10-normalized | .d | 59 to 1721 | 1 to 1663 | | tiling clone, | | 1663/1663 (100 %) | 0 diff (100 %id) |
AL520175 | brain, neuroblastoma cells, Neuroblastoma Cot 10-normalized | .d | 59 to 1015 | 1 to 948 | | fully sequenced, | | 948/948 (100 %) | 8 diff (99.2 %id) |
AL520174 | brain, neuroblastoma cells, Neuroblastoma Cot 10-normalized | .d | 985 to 1721 | 737 to 1 | | fully sequenced, | | 737/737 (100 %) | 29 diff (96.1 %id) |
CN386342 | embryonic stem cells, cell lines H1, H7, andH9 | .e | 1 to 757 | 1 to 756 | E16* | tiling clone, | | 756/756 (100 %) | 3 diff (99.7 %id) |
BQ069693 | brain, neuroblastoma, cell line | .f-u | 1 to 960 | 1 to 969 | G28R V35I P43T S44N V46G ... | tiling clone, | | 969/1019 (95 %) | 32 diff (96.9 %id) |
CV366209 | ovary | .f-u | 761 to 1111 | 2 to 348 | | tiling clone, | | 347/348 (99 %) | 9 diff (97.5 %id) |
BE301834 | Kidney, renal cell adenocarcinoma | .g | 1 to 632 | 1 to 633 | exact | tiling clone, | | 633/633 (100 %) | 5 diff (99.3 %id) |
TI_2016724467 | | Gene ZNF90andRPS16P10, variant not shown | | | | | Suspected internal deletion, this clone was ignored | | |
BX345386 | Neuroblastoma Cot 25-normalized | Gene ZNF90andRPS16P10, variant not shown | | | | | | | |
R89294 | liver and spleen | Gene ZNF90andRPS16P10, variant not shown | | | | | This clone was ignored | | |
? | Gene Summary |
Gene on genome |
mRNA:.a, .b, .c, .d, .e, .f-u, .g |
Alternative mRNAs features, proteins, introns, exons, sequences |
Expression Tissue |
Function, regulation, related genes C |
To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.
If you know more about this gene, or found errors, please share your knowledge. Thank you !