Homo sapiens complex locus LOC100129935, encoding lectin, galactoside-binding, soluble, 14 pseudogene.
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.d), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 6 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is expressed at low level, only 17.6% of the average gene in this release. The sequence of this gene is defined by 23 GenBank accessions from 21 cDNA clones, some from placenta (seen 12 times), embryonic trophoblasts, made from WA01 stemcells (2), placenta normal (2), liver and spleen (once). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 11 distinct gt-ag introns. Transcription produces 6 alternatively spliced mRNAs. There are 3 probable alternative promotors, 3 non overlapping alternative last exons and 3 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of a cassette exon, overlapping exons with different boundaries.
Note that mRNA .cAug10 was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Proteins are expected to localize in cytoplasm. No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
Protein coding potential: 4 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (2 complete, 1 COOH complete, 1 partial), some containing Galactoside-binding lectin domain [Pfam]. The remaining 2 mRNA variants (2 spliced; 1 partial) appear not to encode good proteins.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 19, links to other databases and other names
Map: This gene LOC100129935 maps on chromosome 19, at 19q13.2 according to Entrez Gene. In AceView, it covers 21.97 kb, from 40129325 to 40151290 (NCBI 37, August 2010), on the direct strand.
Links to: the SNP view, gene overviews from Entrez Gene 100129935, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as LOC100129935, FLJ13566.
Closest AceView homologs in other species ?
The closest mouse genes, according to BlastP, are the AceView genes Lgals4 (e=6 10-13), Lgals7 (e=2 10-10).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene lec-4 (e=6 10-10), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene AT1G27120 (e=0.40), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
LOC100129935 Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 0.06 0.11 0.09 0.11 0.12 0.26 0.12 0.15 0.14 0.10 0.18 0.12 0.14 0.13 0.14 0.10 0.19 0.14 0.12 0.10 0.17 0.12 0.12 0.21 0.12 0.13 0.13 0.08 0.07 0.13 0.15 0.18 0.10 0.07 0.09 0.12 0.13 0.21 0.32 0.17 3.33 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene LOC100129935 5' 3' encoded on plus strand of chromosome 19 from 40,129,325 to 40,151,290 32 61 111 51 a [NM] 59 9 61 111 51 b 59 14 7 d 14 111 51 c 59 61 e 2 f 1 2kb 0 207 bp exon 15067 bp [gt-ag] intron 2 GenBank accessions 30 RNA-seq supporting reads 14 Brain 16 Neuroblastoma 225 bp exon 225 bp exon 1906 bp [gt-ag] intron 5 GenBank accessions 56 RNA-seq supporting reads 22 Brain 34 Neuroblastoma (also 3 Primates bodymap) 77 bp exon 500 bp [gt-ag] intron 9 GenBank accessions 102 RNA-seq supporting reads 50 Brain 52 Neuroblastoma (also 2 Primates bodymap) 211 bp exon 1724 bp [gt-ag] intron 8 GenBank accessions 43 RNA-seq supporting reads 18 Brain 25 Neuroblastoma (also 2 Primates bodymap) 253 bp exon 9 accessions, NM_001190441.1 some from placenta (seen 5 times) embryonic trophoblasts made from WA01 stemcells (once) Validated 3' end, 2 accessions 253 bp exon 75 bp exon 505 bp [gt-ag] intron 4 GenBank accessions 55 RNA-seq supporting reads 31 Brain 24 Neuroblastoma (also 12 Primates bodymap) 211 bp exon 15139 bp [gt-ag] intron 1 GenBank accession 8 RNA-seq supporting reads 5 Brain 3 Neuroblastoma 153 bp exon 153 bp exon 1906 bp [gt-ag] intron 5 GenBank accessions 56 RNA-seq supporting reads 22 Brain 34 Neuroblastoma (also 3 Primates bodymap) 77 bp exon 500 bp [gt-ag] intron 9 GenBank accessions 102 RNA-seq supporting reads 50 Brain 52 Neuroblastoma (also 2 Primates bodymap) 211 bp exon 1724 bp [gt-ag] intron 8 GenBank accessions 43 RNA-seq supporting reads 18 Brain 25 Neuroblastoma (also 2 Primates bodymap) 91 bp exon 1 accession from placenta 91 bp exon 1284 bp exon 505 bp [gt-ag] intron 4 GenBank accessions 55 RNA-seq supporting reads 31 Brain 24 Neuroblastoma (also 12 Primates bodymap) 211 bp exon 211 bp exon 136 bp [gt-ag] intron 3 GenBank accessions 11 RNA-seq supporting reads 5 Brain 6 Neuroblastoma 86 bp exon 1245 bp [gt-ag] intron 3 GenBank accessions 4 RNA-seq supporting reads 4 Brain 250 bp exon 6 accessions, some from placenta (seen 4 times) liver and spleen (once) capped 5' end, 1 accession Validated 3' end, 2 accessions 250 bp exon 65 bp exon 65 bp exon 1851 bp [gt-ag] intron 1 GenBank accession 13 RNA-seq supporting reads 3 Brain 10 Neuroblastoma 132 bp exon 500 bp [gt-ag] intron 9 GenBank accessions 102 RNA-seq supporting reads 50 Brain 52 Neuroblastoma (also 2 Primates bodymap) 211 bp exon 211 bp exon 1724 bp [gt-ag] intron 8 GenBank accessions 43 RNA-seq supporting reads 18 Brain 25 Neuroblastoma (also 2 Primates bodymap) 1 accession from embryonic trophoblasts made from WA01 stemcells Validated 3' end, 1 accession 252 bp exon 71 bp exon 505 bp [gt-ag] intron 4 GenBank accessions 55 RNA-seq supporting reads 31 Brain 24 Neuroblastoma (also 12 Primates bodymap) 211 bp exon 211 bp exon 1467 bp [gt-ag] intron 3 GenBank accessions 58 RNA-seq supporting reads 18 Brain 28 Blood 12 Neuroblastoma 2 accessions, some from placenta (seen once) placenta normal (once) 250 bp exon 211 bp exon 211 bp exon 211 bp exon 15144 bp [gt-ag] intron 1 GenBank accession 1 RNA-seq supporting reads 1 Neuroblastoma 1 accession from placenta normal 47 bp exon 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, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . 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.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aAug10 973 bp 142 aa 417 bp 127 bp 2kb possibly including promoter 20170 bp 1kb
bAug10 818 bp 131 aa 424 bp 2kb possibly including promoter 20592 bp 1kb
cAug10 660 bp 76 aa 427 bp 2kb 4735 bp 1kb
dAug10 1831 bp 73 aa 1484 bp 125 bp 2kb including Promoter 3717 bp 1kb
eAug10 532 bp 47 aa 388 bp 2kb 2504 bp 1kb
fAug10 258 bp 46 aa 41 bp 76 bp 2kb 15402 bp 1kb

Gene neighbors and Navigator on chromosome 19q13.2 back to top
NCCRP1 C R C IL28A D C I P IL29 D C I P SAMD4B C I R P P MED29 C I R P ZFP36 D C I R P PLEKHG2 C I R P G SUPT5H C I R P TIMM50 C I R P DLL3 D C R P SELV R P R TDGF7 P LGALS13 D C I R P LOC100129935 C R G LGALS17A C R P LGALS14 C R P LEUTX C P PSMC4 C I R P ZNF546 C R P R C R P SYCN C D C I R P IL28B C I P LRFN1 C I R P GMFG D C I R P PAF1 D C I R P RPS16 I R P EID2B I R P EID2 D C R P CLC D C I R P DYRK1B D C I R P FBL C R P FCGBP C G C G C C R P ZNF780AandZNF780B 100kb 0 PAK4, 390 accessions, 17 variants NCCRP1, 34 accessions 2 variants swarchey, 1 accession IL28A, 14 accessions IL29, 10 accessions, 2 variants SAMD4B, 275 accessions 10 variants kiwari, 1 accession MED29, 408 accessions 5 variants ZFP36, 291 accessions 5 variants PLEKHG2, 262 accessions 17 variants LOC723805, 1 accession SUPT5H, 584 accessions 20 variants TIMM50, 541 accessions 20 variants DLL3, 219 accessions, 6 variants SELV, 12 accessions, 3 variants mukera, 1 accession TDGF7, 1 accession LGALS13, 35 accessions 4 variants LOC100129935, 21 accessions 6 variants LOC100289395, 1 accession LGALS17A, 18 accessions 4 variants LGALS14, 45 accessions 4 variants LEUTX, 6 accessions PSMC4, 484 accessions 10 variants ZNF546, 57 accessions 11 variants chysor, 15 accessions zervoy, 2 accessions snorchey, 1 accession boymee, 1 accession speychey, 2 accessions teesarbo, 1 accession swawvu, 2 accessions kawari, 1 accession jober, 2 accessions shorjer, 1 accession shoyjer, 1 accession swoychey, 1 accession bychor, 1 accession blojer, 1 accession barwu, 4 accessions dochor, 1 accession darchor, 1 accession dawchor, 1 accession feechor, 2 accessions korchor, 2 accessions gorchor, 1 accession kerchor, 2 accessions nawchor, 2 accessions bowu, 3 accessions pachor, 2 accessions puchor, 2 accessions pochor, 1 accession ruseybu, 1 accession cheevoy, 1 accession parchor, 1 accession kuwari, 2 accessions foyvo, 1 accession tuchor, 2 accessions kavo, 1 accession tarchor, 1 accession blorjer, 1 accession reeseybu, 2 accessions korvo, 2 accessions teychor, 1 accession vychor, 2 accessions vochor, 1 accession varchor, 1 accession vawchor, 1 accession rerseybu, 1 accession neevo, 1 accession lormee, 1 accession verchor, 1 accession ryvo, 1 accession wachor, 1 accession wychor, 2 accessions soseybu, 6 accessions wochor, 2 accessions werchor, 1 accession zorchor, 1 accession rawvo, 1 accession chuchor, 3 accessions cheechor, 2 accessions bluchor, 3 accessions glojer, 1 accession zavo, 1 accession flychor, 1 accession glychor, 1 accession sorseybu, 2 accessions seymee, 1 accession zyvo, 1 accession zeevo, 1 accession soyseybu, 1 accession klujer, 2 accessions klychor, 1 accession klochor, 1 accession sheevo, 1 accession klorchor, 1 accession plachor, 2 accessions plochor, 2 accessions pleychor, 1 accession teyseybu, 10 accessions jawber, 4 accessions toyseybu, 1 accession vyseybu, 2 accessions shorvoy, 2 accessions voyseybu, 1 accession raneru, 1 accession plujer, 1 accession blavoy, 3 accessions stuvu, 1 accession spawchey, 1 accession sporchey, 1 accession stoychey, 1 accession pawseybu, 1 accession sweechey, 1 accession perseybu, 2 accessions bachor, 1 accession chavoy, 5 accessions chyvoy, 4 accessions blerjer, 1 accession beyvo, 1 accession borchor, 2 accessions dychor, 2 accessions davo, 1 accession farchor, 1 accession gychor, 1 accession geychor, 8 accessions jeechor, 5 accessions raseybu, 2 accessions dawvo, 1 accession merchor, 1 accession buwu, 1 accession feevo, 1 accession kewari, 1 accession koriru, 4 accessions lymee, 1 accession sawchor, 1 accession tychor, 2 accessions tochor, 2 accessions rarseybu, 1 accession karvo, 1 accession tawchor, 1 accession wusor, 1 accession rawseybu, 2 accessions terchor, 3 accessions lomee, 6 accessions nyvo, 1 accession reyseybu, 2 accessions flerjer, 1 accession glajer, 1 accession veechor, 1 accession kowari, 1 accession rorseybu, 1 accession royseybu, 1 accession voychor, 1 accession weechor, 1 accession zoychor, 1 accession glyjer, 1 accession chochor, 2 accessions chervoy, 3 accessions cheyvoy, 5 accessions sawseybu, 2 accessions raruru, 2 accessions warari, 2 accessions seeseybu, 1 accession blarchor, 1 accession varvo, 1 accession rormee, 1 accession vawvo, 1 accession choyvoy, 1 accession flarchor, 1 accession symee, 1 accession glarjer, 1 accession gluchor, 1 accession glerjer, 1 accession zovo, 1 accession seture, 1 accession tomee, 5 accessions gloychor, 2 accessions glorjer, 3 accessions klyjer, 1 accession klachor, 5 accessions zamee, 2 accessions klerchor, 1 accession kloychor, 1 accession klojer, 1 accession toseybu, 1 accession plychor, 1 accession watore, 1 accession rurari, 1 accession chawtee, 1 accession rerari, 1 accession ratore, 2 accessions, 2 variants terseybu, 1 accession shuvoy, 2 accessions ploychor, 8 accessions skychor, 1 accession blavo, 1 accession vuseybu, 1 accession voseybu, 1 accession varseybu, 1 accession sheyvoy, 7 accessions kloyjer, 1 accession verseybu, 1 accession veyseybu, 2 accessions vorseybu, 1 accession waseybu, 2 accessions wyseybu, 1 accession rorari, 3 accessions shoyvoy, 1 accession woseybu, 1 accession SYCN, 60 accessions, 2 variants klyjar, 5 accessions IL28B, 10 accessions, 2 variants LRFN1, 28 accessions GMFG, 205 accessions, 16 variants PAF1, 528 accessions, 7 variants RPS16, 486 accessions 12 variants EID2B, 36 accessions, 2 variants EID2, 109 accessions CLC, 63 accessions, 2 variants DYRK1B, 159 accessions 7 variants FBL, 356 accessions, 11 variants FCGBP, 298 accessions 7 variants zeysor, 1 accession LOC440525, 65 accessions sheevoy, 3 accessions LOC390933, 2 accessions ZNF780AandZNF780B, 211 accessions 19 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f 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 !