Homo sapiens gene PALMD, encoding palmdelphin and similar to high mobility group box 3.
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SUMMARY back to top
RefSeq annotates one representative transcript from 2 predicted genes that we see see as a single gene (NM included in AceView variant.b), 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 8 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 2.5 times the average gene in this release. The sequence of this gene is defined by 304 GenBank accessions from 253 cDNA clones, some from liver and spleen (seen 27 times), uterus (14), pooled human melanocyte, fetal heart, andpregnant uterus (13), brain (11), lung (10), colon (9), placenta cot 25-normalized (9) and 81 other tissues. We annotate structural defects or features in 5 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 10 distinct gt-ag introns. Transcription produces 10 different mRNAs, 8 alternatively spliced variants and 2 unspliced forms. There are 2 probable alternative promotors, 5 non overlapping alternative last exons and 6 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries, splicing versus retention of one intron.
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant aAug10).
Function: There are 5 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in a process (regulation of cell shape). Proteins are expected to localize in various compartments (nucleus, cytoplasm, membrane).
Protein coding potential: 6 spliced mRNAs putatively encode good proteins, altogether 6 different isoforms (3 complete, 2 COOH complete, 1 partial), some containing paralemmin domain [Pfam], a prenylation domain, a coiled coil stretch [Psort2], apparently vertebrate specific. The remaining 4 mRNA variants (2 spliced, 2 unspliced; 1 partial) appear not to encode good proteins.
Isoform PALMD.cAug10 is annotated using as Met a Kozak-compatible a..AAGg start, thereby gaining 75 amino acids N-terminal to the first AUG. Finally proteins from this gene may be modulated by phosphorylation, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 1, links to other databases and other names
Map: This gene PALMD maps on chromosome 1, at 1p21.2 according to Entrez Gene. In AceView, it covers 52.93 kb, from 100111127 to 100164053 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from PhosphoSite, the SNP view, SNP view, gene overviews from Entrez Gene 100129320, 54873, 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 PALMD, PALML, C1orf11, FLJ20271, LOC100129320, LOC54873, dynoybu or darnoybu, deenoybu. It has been described as palmdelphin, paralemnin-like protein.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Palmd (e= 10-143).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene 2B589 (e=0.33)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
PALMD 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 16.4 5.04 10.1 12.4 21.6 3.57 0.21 0.55 0.59 0.24 5.40 16.4 80.7 8.19 9.41 12.4 9.41 46.3 24.8 18.8 10.8 0.55 2.52 1.55 17.6 1.45 0.27 0.18 4.71 0.59 11.6 10.1 14.3 13.3 0.96 0.68 1.78 2.90 35.1 2.70 7.13 1.26 1.66 1.45 1.10 2.19 8.19 35.1 3.57 32.8 21.6 0.83 1.10 0.17 2.05 3.82 30.6 1.18 1.18 3.82 1.91 1.78 8.19 0.59 17.6 1.78 18.8 16.4 5.04 1.91 1.78 1.91 5.04 1.91 17.6 2.70 12.4 3.82 2.90 9.41 2.19 2.90 26.6 1.66 2.70 12.4 2.35 21.6 2.35 8.19 20.2 1.26 14.3 1.91 2.19 16.4 8.78 2.90 53.2 16.4 5.40 4.71 0.36 1.66 2.52 2.05 21.6 3.10 2.35 10.1 5.40 32.8 1.66 3.57 3.33 0.55 5.79 24.8 2.35 21.6 0.78 5.04 10.1 2.90 1.55 2.70 14.3 11.6 8.19 7.13 4.71 0.83 17.6 8.19 6.65 1.78 23.2 2.90 8.19 17.6 11.6 3.33 3.82 1.91 0.83 0.45 0.48 2.52 5.04 1.91 1.18 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 PALMD 5' 3' encoded on plus strand of chromosome 1 from 100,111,127 to 100,164,053 8235 9255 10515 11253 9671 8172 a 8235 9255 10515 11253 9671 8172 13902 b [NM] 11253 9671 8172 13902 c 34 8235 9255 10515 e 8 d 8235 9255 10515 11253 9671 h 8 f j-u g-u 8235 9255 10515 11253 i 1 2kb 0 170 bp exon 170 bp exon 48 bp uORF 170 bp exon 170 bp exon 15956 bp [gt-ag] intron 116 GenBank accessions 8119 RNA-seq supporting reads 1532 UHR pooled cells 1036 Brain 3 Blood 5402 Neuroblastoma 146 Other (also 8679 Primates bodymap) 81 bp exon 81 bp exon 5242 bp [gt-ag] intron 112 GenBank accessions 9143 RNA-seq supporting reads 1833 UHR pooled cells 1218 Brain 9 Blood 5921 Neuroblastoma 162 Other (also 9700 Primates bodymap) 125 bp exon 125 bp exon 18909 bp [gt-ag] intron 106 GenBank accessions 10409 RNA-seq supporting reads 2049 UHR pooled cells 1274 Brain 5 Blood 6871 Neuroblastoma 210 Other (also 7405 Primates bodymap) 115 bp exon 115 bp exon 139 bp [gt-ag] intron 79 GenBank accessions 11174 RNA-seq supporting reads 2185 UHR pooled cells 1320 Brain 6 Blood 7479 Neuroblastoma 184 Other (also 6385 Primates bodymap) 34 bp exon 34 bp exon 112 bp [gt-ag] intron 61 GenBank accessions 9610 RNA-seq supporting reads 1900 UHR pooled cells 1109 Brain 4 Blood 6417 Neuroblastoma 180 Other (also 5218 Primates bodymap) 114 bp exon 114 bp exon 1585 bp [gt-ag] intron 36 GenBank accessions 8136 RNA-seq supporting reads 1744 UHR pooled cells 914 Brain 5322 Neuroblastoma 156 Other (also 6739 Primates bodymap) 1303 bp exon 1303 bp exon 2 accessions, some from fetal brain (seen 2 times) brain (once) 1303 bp exon 586 bp exon 586 bp exon 15956 bp [gt-ag] intron 116 GenBank accessions 8119 RNA-seq supporting reads 1532 UHR pooled cells 1036 Brain 3 Blood 5402 Neuroblastoma 146 Other (also 8679 Primates bodymap) 81 bp exon 5242 bp [gt-ag] intron 112 GenBank accessions 9143 RNA-seq supporting reads 1833 UHR pooled cells 1218 Brain 9 Blood 5921 Neuroblastoma 162 Other (also 9700 Primates bodymap) 125 bp exon 18909 bp [gt-ag] intron 106 GenBank accessions 10409 RNA-seq supporting reads 2049 UHR pooled cells 1274 Brain 5 Blood 6871 Neuroblastoma 210 Other (also 7405 Primates bodymap) 115 bp exon 139 bp [gt-ag] intron 79 GenBank accessions 11174 RNA-seq supporting reads 2185 UHR pooled cells 1320 Brain 6 Blood 7479 Neuroblastoma 184 Other (also 6385 Primates bodymap) 34 bp exon 112 bp [gt-ag] intron 61 GenBank accessions 9610 RNA-seq supporting reads 1900 UHR pooled cells 1109 Brain 4 Blood 6417 Neuroblastoma 180 Other (also 5218 Primates bodymap) 114 bp exon 1585 bp [gt-ag] intron 36 GenBank accessions 8136 RNA-seq supporting reads 1744 UHR pooled cells 914 Brain 5322 Neuroblastoma 156 Other (also 6739 Primates bodymap) 1098 bp exon 4146 bp [gt-ag] intron 72 GenBank accessions 13830 RNA-seq supporting reads 3445 UHR pooled cells 1546 Brain 3 Blood 8722 Neuroblastoma 114 Other (also 5831 Primates bodymap) 1131 bp exon 217 accessions, NM_017734.4 some from liver and spleen (seen 24 times) pooled human melanocyte fetal heart, andpregnant uterus (12) uterus (12), placenta cot 25-normalized (9) lung (8) capped 5' end, 50 accessions Validated 3' end, 25 accessions Validated 3' end, 6 accessions 1131 bp exon 3694 bp exon 3694 bp exon 139 bp [gt-ag] intron 79 GenBank accessions 11174 RNA-seq supporting reads 2185 UHR pooled cells 1320 Brain 6 Blood 7479 Neuroblastoma 184 Other (also 6385 Primates bodymap) 34 bp exon 112 bp [gt-ag] intron 61 GenBank accessions 9610 RNA-seq supporting reads 1900 UHR pooled cells 1109 Brain 4 Blood 6417 Neuroblastoma 180 Other (also 5218 Primates bodymap) 114 bp exon 1585 bp [gt-ag] intron 36 GenBank accessions 8136 RNA-seq supporting reads 1744 UHR pooled cells 914 Brain 5322 Neuroblastoma 156 Other (also 6739 Primates bodymap) 1098 bp exon 4146 bp [gt-ag] intron 72 GenBank accessions 13830 RNA-seq supporting reads 3445 UHR pooled cells 1546 Brain 3 Blood 8722 Neuroblastoma 114 Other (also 5831 Primates bodymap) 361 bp exon 18 accessions, some from placenta normal (seen 5 times) liver and spleen (3) ovary (3), 2 pooled high-grade transitional celltumors (once) amygdala (once) Validated 3' end, 1 accession 361 bp exon 223 bp exon 460 bp [gt-ag] intron 1 GenBank accession 33 RNA-seq supporting reads 6 UHR pooled cells 12 Brain 15 Neuroblastoma (also 28 Primates bodymap) 109 bp exon 109 bp exon 15956 bp [gt-ag] intron 116 GenBank accessions 8119 RNA-seq supporting reads 1532 UHR pooled cells 1036 Brain 3 Blood 5402 Neuroblastoma 146 Other (also 8679 Primates bodymap) 81 bp exon 5242 bp [gt-ag] intron 112 GenBank accessions 9143 RNA-seq supporting reads 1833 UHR pooled cells 1218 Brain 9 Blood 5921 Neuroblastoma 162 Other (also 9700 Primates bodymap) 125 bp exon 18909 bp [gt-ag] intron 106 GenBank accessions 10409 RNA-seq supporting reads 2049 UHR pooled cells 1274 Brain 5 Blood 6871 Neuroblastoma 210 Other (also 7405 Primates bodymap) 35 bp exon 1 accession from uterus capped 5' end, 1 accession 35 bp exon 1035 bp exon 1035 bp exon 4153 bp [gt-ag] intron 1 GenBank accession 7 RNA-seq supporting reads 2 UHR pooled cells 3 Brain 2 Neuroblastoma (also 1 Primates bodymap) 348 bp exon 1 accession from brain from glioblastoma (pooled) Validated 3' end, 1 accession 348 bp exon 418 bp exon 418 bp exon 15956 bp [gt-ag] intron 116 GenBank accessions 8119 RNA-seq supporting reads 1532 UHR pooled cells 1036 Brain 3 Blood 5402 Neuroblastoma 146 Other (also 8679 Primates bodymap) 81 bp exon 5242 bp [gt-ag] intron 112 GenBank accessions 9143 RNA-seq supporting reads 1833 UHR pooled cells 1218 Brain 9 Blood 5921 Neuroblastoma 162 Other (also 9700 Primates bodymap) 125 bp exon 18909 bp [gt-ag] intron 106 GenBank accessions 10409 RNA-seq supporting reads 2049 UHR pooled cells 1274 Brain 5 Blood 6871 Neuroblastoma 210 Other (also 7405 Primates bodymap) 115 bp exon 139 bp [gt-ag] intron 79 GenBank accessions 11174 RNA-seq supporting reads 2185 UHR pooled cells 1320 Brain 6 Blood 7479 Neuroblastoma 184 Other (also 6385 Primates bodymap) 34 bp exon 112 bp [gt-ag] intron 61 GenBank accessions 9610 RNA-seq supporting reads 1900 UHR pooled cells 1109 Brain 4 Blood 6417 Neuroblastoma 180 Other (also 5218 Primates bodymap) 6 accessions, some from lung (seen once) metastatic chondrosarcoma (once) pooled brain, lung, testis (once) Validated 3' end, 2 accessions 120 bp exon 190 bp exon 8420 bp [gt-ag] intron 2 GenBank accessions 6 RNA-seq supporting reads 1 Brain 5 Neuroblastoma (also 11 Primates bodymap) 202 bp exon 2 accessions 202 bp exon 527 bp exon 527 bp exon 1 accession from prostate capped 5' end, 1 accession 527 bp exon 2228 bp exon 2228 bp exon 9 accessions, some from colon (seen 6 times) testis (3) 2228 bp exon 301 bp exon 15956 bp [gt-ag] intron 116 GenBank accessions 8119 RNA-seq supporting reads 1532 UHR pooled cells 1036 Brain 3 Blood 5402 Neuroblastoma 146 Other (also 8679 Primates bodymap) 81 bp exon 5242 bp [gt-ag] intron 112 GenBank accessions 9143 RNA-seq supporting reads 1833 UHR pooled cells 1218 Brain 9 Blood 5921 Neuroblastoma 162 Other (also 9700 Primates bodymap) 125 bp exon 125 bp exon 18909 bp [gt-ag] intron 106 GenBank accessions 10409 RNA-seq supporting reads 2049 UHR pooled cells 1274 Brain 5 Blood 6871 Neuroblastoma 210 Other (also 7405 Primates bodymap) 115 bp exon 115 bp exon 139 bp [gt-ag] intron 79 GenBank accessions 11174 RNA-seq supporting reads 2185 UHR pooled cells 1320 Brain 6 Blood 7479 Neuroblastoma 184 Other (also 6385 Primates bodymap) 3 accessions, some from trabecular meshwork (seen once) uterus (once) capped 5' end, 2 accessions 10 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 uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aAug10 1942 bp 551 aa 125 bp 161 bp 45 bp 2kb possibly including promoter 43885 bp 1kb
bAug10 3284 bp 551 aa 541 bp 1087 bp 2kb including Promoter 49373 bp 1kb
cAug10 5301 bp 450 aa 3631 bp 317 bp 2kb possibly including promoter 11283 bp 1kb
dAug10 1383 bp 345 aa 343 bp 2kb 5536 bp 1kb
eAug10 573 bp 95 aa 287 bp 2kb including Promoter 41140 bp 1kb
fAug10 392 bp 68 aa 185 bp 2kb 8812 bp 1kb
gAug10-unspliced 2228 bp 71 aa 84 bp 1928 bp 2kb 2228 bp 1kb
hAug10 893 bp 63 aa 701 bp 2kb 41251 bp 1kb
iAug10 632 bp 36 aa 402 bp 119 bp 2kb including Promoter 40878 bp 1kb
jAug10-unspliced 527 bp 30 aa 8 bp 426 bp 2kb including Promoter 527 bp 1kb

Gene neighbors and Navigator on chromosome 1p21.2 back to top
LPPR4 D C I R P PALMD D C R P AGL D C I R P SLC35A3 D C R P R HIAT1 C R P C CCDC76 C I R P C R P FRRS1 R G R C I R P SASS6 100kb 0 LPPR4, 152 accessions 3 variants PALMD, 275 accessions 10 variants AGL, 249 accessions, 10 variants SLC35A3, 107 accessions 10 variants sparber, 82 accessions HIAT1, 205 accessions 7 variants tomima, 1 accession CCDC76, 171 accessions 13 variants suruha, 2 accessions, 2 variants swoynorbu, 1 accession smarmeebo, 1 accession flerlor, 3 accessions bonoybu, 1 accession jupubu, 1 accession smawmeebo, 1 accession seruha, 1 accession smeemeebo, 2 accessions smermeebo, 2 accessions snarber, 5 accessions bernoybu, 1 accession soruha, 3 accessions, 2 variants gyplu, 1 accession bornoybu, 1 accession boynoybu, 2 accessions danoybu, 1 accession donoybu, 2 accessions smoymeebo, 1 accession funoybu, 2 accessions fernoybu, 2 accessions foynoybu, 1 accession gynoybu, 2 accessions snomeebo, 1 accession gonoybu, 1 accession snarmeebo, 1 accession snawmeebo, 1 accession florlor, 1 accession geenoybu, 1 accession rapubu, 1 accession rypubu, 1 accession sneemeebo, 1 accession temima, 2 accessions berzerbo, 1 accession geyplu, 1 accession gernoybu, 1 accession geynoybu, 1 accession sayaro, 6 accessions snarroybo, 2 accessions gornoybu, 1 accession spawber, 19 accessions goynoybu, 2 accessions janoybu, 1 accession gorplu, 1 accession jynoybu, 1 accession spymeebo, 2 accessions dyzerbo, 1 accession jarnoybu, 2 accessions goyplu, 1 accession snawroybo, 13 accessions speeber, 19 accessions sparmeebo, 1 accession karuha, 2 accessions, 2 variants japlu, 2 accessions duzerbo, 1 accession spermeebo, 1 accession banoybu, 2 accessions snuber, 1 accession bynoybu, 1 accession bunoybu, 1 accession barnoybu, 2 accessions smeymeebo, 1 accession beenoybu, 1 accession dunoybu, 2 accessions dernoybu, 1 accession snawber, 4 accessions guplu, 8 accessions karpubu, 1 accession sneeber, 12 accessions fanoybu, 1 accession sheywybo, 2 accessions fynoybu, 1 accession snymeebo, 1 accession morpubu, 3 accessions farnoybu, 1 accession pawpubu, 1 accession snumeebo, 1 accession feynoybu, 1 accession ganoybu, 1 accession poypubu, 1 accession tumima, 1 accession garnoybu, 6 accessions rerpubu, 1 accession sopubu, 1 accession gerplu, 2 accessions beyzerbo, 3 accessions snormeebo, 3 accessions snoymeebo, 4 accessions borzerbo, 1 accession boyzerbo, 1 accession dazerbo, 1 accession junoybu, 2 accessions jonoybu, 1 accession serpubu, 1 accession jernoybu, 1 accession jornoybu, 1 accession joynoybu, 1 accession kanoybu, 3 accessions sneeroybo, 1 accession teypubu, 1 accession spoyber, 9 accessions warpubu, 1 accession FRRS1, 30 accessions, 6 variants spyber, 6 accessions, 3 variants LOC730081, 21 accessions 2 variants SASS6, 68 accessions, 5 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               5 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g-u, .h, .i, .j-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DC

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'.

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