Homo sapiens gene AFM, encoding afamin.
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SUMMARY back to top
RefSeq summary
[AFM] This gene is a member of the albumin gene family, which is comprised of four genes that localize to chromosome 4 in a tandem arrangement. These four genes encode structurally-related serum transport proteins that are known to be evolutionarily related. The protein encoded by this gene is regulated developmentally, expressed in the liver and secreted into the bloodstream. [provided by RefSeq].

RefSeq annotates one representative transcript (NM included in AceView variant.a), 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 5 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 0.7 times the average gene in this release. The sequence of this gene is defined by 75 GenBank accessions from 74 cDNA clones, some from kidney (seen 27 times), liver (18), corresponding non cancerous liver tissue (11), liver and spleen (4), liver, tumor tissue (3), breast (2), heart (2) and 5 other tissues. We annotate structural defects or features in 6 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 16 distinct gt-ag introns. Transcription produces 7 different mRNAs, 5 alternatively spliced variants and 2 unspliced forms. There are 2 probable alternative promotors, 3 non overlapping alternative last exons and 2 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.
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 dAug10).
Function: There are 18 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in a process (transport). Proteins are expected to localize in various compartments (extracellular space, extracellular region).
Protein coding potential: 4 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (2 complete, 1 COOH complete, 1 partial), some containing Serum albumin family domain [Pfam], a second peroximal domain, a vacuolar domain, a coiled coil stretch [Psort2]; the 2 complete proteins appear to be secreted. The remaining 3 mRNA variants (1 spliced, 2 unspliced; 1 partial) appear not to encode good proteins. Finally proteins from this gene may be modulated by acetylation; 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 4, links to other databases and other names
Map: This gene AFM maps on chromosome 4, at 4q13.3 according to Entrez Gene. In AceView, it covers 22.32 kb, from 74347400 to 74369724 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 173, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC. The previous AceView annotation is here.
Other names: The gene is also known as AFM, ALF, ALB2, ALBA, MGC125338 or MGC125339, LOC173. It has been described as afamin, alpha-Alb, alpha-albumin.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Afm (e=6 10-42)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
AFM 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 21.6 371 2.70 131 0.04 0.42 397 489 323 0.15 0.18 262 562 0.59 0.72 0.16 106 0.17 0.15 0.09 2.05 0.13 0.11 0.72 131 0.29 0.51 0.21 1.45 65.5 0.10 0.13 0.10 0.18 0.16 106 795 0.48 0.78 0.09 161 1.18 49.7 0.29 692 0.29 0.11 0.13 0.10 28.5 262 0.09 0.07 46.3 0.48 0.34 86.5 524 0.16 0.16 0.24 0.19 0.18 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 AFM 5' 3' encoded on plus strand of chromosome 4 from 74,347,400 to 74,369,724 1115 1156 878 1557 1827 1511 1110 1805 2099 2049 1893 2327 2141 1394 a [NM] 1115 1156 447 d 1110 1805 2099 b e-u 2099 56 1893 c g-u 2099 2049 f 1 2kb 0 181 bp exon 181 bp exon 2077 bp [gt-ag] intron 36 GenBank accessions 1079 RNA-seq supporting reads 6 UHR pooled cells 1073 Neuroblastoma (also 6350 Primates bodymap) 49 bp exon 268 bp [gt-ag] intron 36 GenBank accessions 1120 RNA-seq supporting reads 2 UHR pooled cells 1118 Neuroblastoma (also 26448 Primates bodymap) 133 bp exon 1471 bp [gt-ag] intron 32 GenBank accessions 846 RNA-seq supporting reads 2 UHR pooled cells 844 Neuroblastoma (also 17251 Primates bodymap) 212 bp exon 893 bp [gt-ag] intron 38 GenBank accessions 1519 RNA-seq supporting reads 13 UHR pooled cells 1506 Neuroblastoma (also 14950 Primates bodymap) 133 bp exon 624 bp [gt-ag] intron 12 GenBank accessions 1815 RNA-seq supporting reads 10 UHR pooled cells 1805 Neuroblastoma (also 20658 Primates bodymap) 98 bp exon 808 bp [gt-ag] intron 10 GenBank accessions 1501 RNA-seq supporting reads 6 UHR pooled cells 1495 Neuroblastoma (also 16330 Primates bodymap) 130 bp exon 3112 bp [gt-ag] intron 10 GenBank accessions 1100 RNA-seq supporting reads 8 UHR pooled cells 1092 Neuroblastoma (also 17304 Primates bodymap) 215 bp exon 3213 bp [gt-ag] intron 10 GenBank accessions 1795 RNA-seq supporting reads 15 UHR pooled cells 1780 Neuroblastoma (also 18319 Primates bodymap) 133 bp exon 2219 bp [gt-ag] intron 13 GenBank accessions 2086 RNA-seq supporting reads 12 UHR pooled cells 2074 Neuroblastoma (also 20563 Primates bodymap) 98 bp exon 1364 bp [gt-ag] intron 9 GenBank accessions 2040 RNA-seq supporting reads 18 UHR pooled cells 2022 Neuroblastoma (also 9344 Primates bodymap) 133 bp exon 757 bp [gt-ag] intron 13 GenBank accessions 1880 RNA-seq supporting reads 7 UHR pooled cells 1873 Neuroblastoma (also 16355 Primates bodymap) 224 bp exon 1559 bp [gt-ag] intron 16 GenBank accessions 2311 RNA-seq supporting reads 12 UHR pooled cells 2299 Neuroblastoma (also 10938 Primates bodymap) 133 bp exon 1130 bp [gt-ag] intron 18 GenBank accessions 2123 RNA-seq supporting reads 14 UHR pooled cells 2109 Neuroblastoma (also 13253 Primates bodymap) 61 bp exon 61 bp exon 765 bp [gt-ag] intron 14 GenBank accessions 1380 RNA-seq supporting reads 9 UHR pooled cells 1 Brain 1370 Neuroblastoma (also 819 Primates bodymap) 56 accessions, NM_001133.2 some from kidney (seen 22 times) liver (16), corresponding non cancerous liver tissue (5) liver, tumor tissue (3) breast (2) capped 5' end, 22 accessions Validated 3' end, 4 accessions 132 bp exon 113 bp exon 113 bp exon 21 bp uORF 113 bp exon 113 bp exon 2077 bp [gt-ag] intron 36 GenBank accessions 1079 RNA-seq supporting reads 6 UHR pooled cells 1073 Neuroblastoma (also 6350 Primates bodymap) 49 bp exon 49 bp exon 268 bp [gt-ag] intron 36 GenBank accessions 1120 RNA-seq supporting reads 2 UHR pooled cells 1118 Neuroblastoma (also 26448 Primates bodymap) 133 bp exon 133 bp exon 1050 bp [gt-ag] intron 2 GenBank accessions 445 RNA-seq supporting reads 2 UHR pooled cells 443 Neuroblastoma (also 394 Primates bodymap) 233 bp exon 233 bp exon 1 accession from liver capped 5' end, 1 accession 233 bp exon 102 bp exon 3112 bp [gt-ag] intron 10 GenBank accessions 1100 RNA-seq supporting reads 8 UHR pooled cells 1092 Neuroblastoma (also 17304 Primates bodymap) 215 bp exon 3213 bp [gt-ag] intron 10 GenBank accessions 1795 RNA-seq supporting reads 15 UHR pooled cells 1780 Neuroblastoma (also 18319 Primates bodymap) 133 bp exon 2219 bp [gt-ag] intron 13 GenBank accessions 2086 RNA-seq supporting reads 12 UHR pooled cells 2074 Neuroblastoma (also 20563 Primates bodymap) 317 bp exon 4 accessions, some from kidney (seen 4 times) Validated 3' end, 3 accessions 317 bp exon 806 bp exon 806 bp exon 4 accessions, some from liver and spleen (seen 4 times) 806 bp exon 14 bp exon 2219 bp [gt-ag] intron 13 GenBank accessions 2086 RNA-seq supporting reads 12 UHR pooled cells 2074 Neuroblastoma (also 20563 Primates bodymap) 42 bp exon 1420 bp [gt-ag] intron 1 GenBank accession 55 RNA-seq supporting reads 55 Neuroblastoma (also 187 Primates bodymap) 133 bp exon 757 bp [gt-ag] intron 13 GenBank accessions 1880 RNA-seq supporting reads 7 UHR pooled cells 1873 Neuroblastoma (also 16355 Primates bodymap) 224 bp exon 1 accession from corresponding non cancerous liver tissue 224 bp exon 402 bp exon 402 bp exon 1 accession from kidney 402 bp exon 321 bp exon 2219 bp [gt-ag] intron 13 GenBank accessions 2086 RNA-seq supporting reads 12 UHR pooled cells 2074 Neuroblastoma (also 20563 Primates bodymap) 98 bp exon 98 bp exon 1364 bp [gt-ag] intron 9 GenBank accessions 2040 RNA-seq supporting reads 18 UHR pooled cells 2022 Neuroblastoma (also 9344 Primates bodymap) 2 accessions, some from corresponding non cancerous liver tissue (seen 2 times) 67 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 2065 bp 599 aa 93 bp 172 bp 2kb including Promoter 22325 bp 1kb
bAug10 767 bp 237 aa 53 bp 2kb 9311 bp 1kb
cAug10 413 bp 137 aa 2kb 4809 bp 1kb
dAug10 528 bp 107 aa 25 bp 179 bp 18 bp 2kb including Promoter 3923 bp 1kb
eAug10-unspliced 806 bp 40 aa 106 bp 577 bp 2kb 806 bp 1kb
fAug10 486 bp 42 aa 360 bp 2kb 4069 bp 1kb
gAug10-unspliced 402 bp 29 aa 33 bp 279 bp 2kb 402 bp 1kb

Gene neighbors and Navigator on chromosome 4q13.3 back to top
HMGA1L2 P R ALB D C I R P AFP D C I R P AFM C R P R IL8 D I R P CXCL6andPPBPL1 D C I R P PF4V1 C P CXCL1 D C I R P D C R P COX18 C I R P ANKRD17 C D C R P RASSF6 100kb 0 HMGA1L2, 2 accessions lorsmaby, 41 accessions 2 variants ALB, 558 accessions, 23 variants AFP, 198 accessions, 8 variants AFM, 74 accessions, 7 variants guswaby, 14 accessions 3 variants IL8, 328 accessions, 5 variants CXCL6andPPBPL1, 178 accessions 3 variants PF4V1, 6 accessions CXCL1, 178 accessions 5 variants kleyspawbu, 1 accession roysmuby, 1 accession plerswerbu, 1 accession dawskyby, 1 accession skyspawbu, 1 accession feyskyby, 2 accessions skerspawbu, 1 accession ployswerbu, 2 accessions tikime, 7 accessions sorsmuby, 1 accession soysmuby, 1 accession tysmuby, 1 accession smuspawbu, 1 accession tosmuby, 1 accession snaspawbu, 1 accession teysmuby, 1 accession vusmuby, 1 accession jaskyby, 1 accession versmuby, 1 accession steespawbu, 1 accession karskyby, 1 accession skoyswerbu, 1 accession keeskyby, 2 accessions berspeebu, 2 accessions dyspeebu, 3 accessions keyskyby, 1 accession puskyby, 2 accessions wosmuby, 1 accession norskyby, 4 accessions weysmuby, 2 accessions dospeebu, 1 accession dawspeebu, 1 accession zusmuby, 1 accession ruskyby, 3 accessions slerswerbu, 2 accessions sleyswerbu, 2 accessions zeesmuby, 3 accessions sloyswerbu, 2 accessions totore, 7 accessions roskyby, 1 accession savobo, 1 accession zersmuby, 1 accession zoysmuby, 3 accessions tekime, 1 accession syvobo, 1 accession reyskyby, 1 accession chusmuby, 1 accession seyskyby, 1 accession garspeebu, 1 accession charsmuby, 1 accession worsweebu, 2 accessions smoyswerbu, 1 accession lyglu, 3 accessions chorsmuby, 1 accession snawswerbu, 1 accession shusmuby, 1 accession snerswerbu, 2 accessions snorswerbu, 1 accession verskyby, 2 accessions sovobo, 1 accession shoysmuby, 1 accession blasmuby, 2 accessions gerspeebu, 2 accessions sparswerbu, 2 accessions blusmuby, 1 accession blosmuby, 1 accession sehoyu, 1 accession bleesmuby, 1 accession blersmuby, 2 accessions blorsmuby, 1 accession tanuyu, 1 accession flasmuby, 1 accession sperswerbu, 1 accession speyswerbu, 1 accession kleespawbu, 1 accession plaspawbu, 1 accession pleeswerbu, 2 accessions kloflor, 3 accessions plerspawbu, 1 accession rorsmuby, 3 accessions sasmuby, 1 accession pleyspawbu, 1 accession skuspawbu, 3 accessions sysmuby, 2 accessions plorswerbu, 1 accession sarsmuby, 2 accessions skospawbu, 1 accession skorspawbu, 2 accessions nenuyu, 2 accessions seysmuby, 3 accessions bloyku, 4 accessions tasmuby, 1 accession vogy, 7 accessions, 2 variants forskyby, 1 accession gawskyby, 1 accession smospawbu, 1 accession smerspawbu, 1 accession kleeflor, 2 accessions smeyspawbu, 1 accession tarsmuby, 2 accessions tawsmuby, 3 accessions teesmuby, 1 accession tersmuby, 1 accession snerspawbu, 1 accession torsmuby, 1 accession toysmuby, 3 accessions skuswerbu, 2 accessions snoyspawbu, 1 accession skoswerbu, 1 accession vasmuby, 6 accessions vysmuby, 1 accession skarswerbu, 1 accession varsmuby, 1 accession vawsmuby, 3 accessions skawswerbu, 1 accession skeeswerbu, 1 accession jawskyby, 1 accession veysmuby, 1 accession swoyspawbu, 1 accession vorsmuby, 2 accessions skorswerbu, 1 accession leysmaby, 5 accessions kerskyby, 1 accession slyswerbu, 2 accessions wysmuby, 2 accessions royvobo, 2 accessions korskyby, 1 accession wusmuby, 4 accessions wawsmuby, 2 accessions paskyby, 1 accession wersmuby, 1 accession pawskyby, 5 accessions kloyflor, 2 accessions tukime, 2 accessions worsmuby, 1 accession darspeebu, 1 accession farswaby, 7 accessions soso, 24 accessions slawswerbu, 1 accession sleeswerbu, 2 accessions plarflor, 1 accession zawsmuby, 2 accessions derspeebu, 1 accession plawflor, 5 accessions zeysmuby, 1 accession zorsmuby, 2 accessions chasmuby, 5 accessions rorskyby, 1 accession chosmuby, 1 accession smeeswerbu, 1 accession teyskyby, 2 accessions vaskyby, 1 accession gaswaby, 1 accession vyskyby, 1 accession geespeebu, 1 accession flerku, 2 accessions sheysmuby, 1 accession spyswerbu, 1 accession spuswerbu, 1 accession nonuyu, 1 accession floyku, 5 accessions ployflor, 1 accession blysmuby, 1 accession voyskyby, 1 accession blarsmuby, 1 accession veygy, 2 accessions bleysmuby, 1 accession choskyby, 1 accession spawswerbu, 1 accession flysmuby, 1 accession flusmuby, 1 accession COX18, 153 accessions 6 variants ANKRD17, 451 accessions 19 variants zysmuby, 1 accession RASSF6, 110 accessions 9 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               18 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e-u, .f, .g-u 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'.

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