Original terms

• AS affecting protein function - Alternative splicing which cause functional annotation changes such as protein motif, GO, subceller localization signal and transmembrane domain. Protein motif and GO were predicted by InterProScan, subceller localization signal was predicted by WoLF PSORT and TargetP and transmembrane domain was predicted by TMHMM and SOSUI.
• AS initiation/termination - AS patterns regarding initiation or termination of transcripts. See Scheme of AS variant decision.
• AS location - The place of locus where AS events occur on genome. There are 5'/3'-end and Internal. See Scheme of AS variant decision.
• AS pattern - There are five traditional patterns such as cassette (skipped exon), internal acceptor (alternative 3' splice), internal donor (alternative 5' splice), mutually exclusive and retaied intron. See Scheme of AS variant decision.
• AS region - The classification of AS variant whose AS exons are in the coding region or 5'/3' untranslated region.
• Bridged - One of the complex AS patterns. Two AS variants were arrayed tandemly without sharing any exons and another transcript 'bridged' them, sharing at least some of its exons with both of them and also sharing the same reading frame to their ORFs.
• Complex AS pattern - Phenomenon which produces totally different proteins by alternative splicing from same locus. We identified three patterns such as bridged, nested and multiple CDS.
• Conserved AS - AS variants which two or more different ESVs exist in both human and mouse locus. See Scheme of genomic comparison
• Difference in length of encoded protein - Average amino acid length of difference in protein coding region on genome among RASVs which have only full-length ORF.
• Equally-spliced variant (ESV) - Among transcript-conserved variants, combination of exons is same in human and mouse. See Scheme of genomic comparison
• Functional annotation - Ptotein functions annotated to full-length ORFs. We used four protein functions such as protein motif, GO, subcellular localization signal and transmembrane domain.
• Genome-conserved - In exon, the full-length or CDS in exon is mapped on human-mouse genome alignment with over threshold (Coverange=70% and Identity=60%) but not mapped or mapped with under the threshold on the alignment. In variant, non-conserved exons are nothing and at least one genome-conserved exon exists. See Scheme of genomic comparison
• H-Invitational - The human full-length cDNA annotation meeting. The aims were collecting information regarding human full-lengh cDNAs and annotating them by biologists invited from all over the world. It has held two times in Tokyo, Japan in 2002 and 2003.
• HIT - H-Invitational transcript ID. Each H-Invitational cDNA entry is assigned an HIT ID, a stable and unique indintifier for each H-Invitational transcript.
• HIX - H-Invitational cluster (locus) ID. Each H-Invitational locus is assigned HIX ID, a stable and unique identifier for each H-Invitational locus.
• Multiple CDS - One of the complex AS patterns. Different ORFs >200 bp in length were annotated independently for different AS variants sharing at least some of the exons but not sharing any reading frame.
• Nested - One of the complex AS patterns. CDS region of one AS variant was not shared with another variant.
• Non-conserved - In exon, the full-length or CDS in exon is not mapped on human-mouse genome alignment or mapped on it with under threshold (Coverange=70% and Identity=60%). In variant, at least one non-conserved exon exists. See Scheme of genomic comparison
• RASV - Abbreviation of representative AS variant. It means that the representative among AS variants whose genomic structures are same. They were finally identified by the median of the cover range on genome. See Flowchart of RASV decision.
• Transcript-conserved - In exon, the full-length or CDS in exon is mapped on human-mouse genome alignment with over threshold (Coverange=70% and Identity=60%) and mapped on the mouse counterpart exon with over the same threshold. In variant, all exons are transcript-conserved ones. See Scheme of genomic comparison
• Truncated transcript - Transcripts which do not seem to be full-length. See Scheme of truncated transcript decision.

General terms

• Alternative splicing - It is a phenomenon in which different combinations of exons are spliced to produce distinct transcripts. Abbreviated as AS.
• AS - Abbreviation of alternative splicing.
• CDS - Abbreviation of coding sequence. Full-length ORF is regarded as CDS.
• Cassette (Skipped exon) - One of the AS patterns. See Scheme of AS variant decision.
• ESE - Abbreviation of exonic splicing enhancer. Hexabasic sequences located in exon for mRNA splicing. They were identified by RESCUE-ESE.
• Full-length cDNA - cDNA which were sequenced by validated method like oligo-capping.
• GO - Abbreviation of Gene ontology. The web site is http://www.geneontology.org/.
• Internal acceptor (Alternative 3' splice) - One of the AS patterns. See Scheme of AS variant decision.
• Internal donor (Alternative 5' splice) - One of the AS patterns. See Scheme of AS variant decision.
• Mutually exclusive - One of the AS patterns. See Scheme of AS variant decision.
• ncRNA - Abbreviation of non-coding RNA.
• NMD - Abbreviation of nonsense-mediated mRNA decay. It was selected as variants in which the stop codon mapped more than 50 bp upstream of the last exon-exon junction.
• ORF - Abbreviation of open reading frame.
• Protein motif - Functional parts within amino acid sequences. They were predicted by InterProScan which is protein functional analysis program.
• Retained intron - One of the AS patterns. See Scheme of AS variant decision.
• Retrotransposon - Genomic elements which can duplicate themselves by reverse-transcription. There are two types such as LTR and Non-LTR (LINE and SINE). They were identified by RepeatMasker.
• Splice-site sequences - 5'-GT-AG-3' is dominant splice-site sequences of intron in human. This type of intron is spliced by U2 snRNP. There are a few minor types of splice-site sequences such as 5'-GC-AG-3' and 5'-AT-AC-3' (U12-type).
• Subcell - Abbreviation of subcellular localization signal.
• Subcellular localization signal - The place where the protein exists in the cell by detecting the signal sequences. We used the data predicted by two programs such as WoLF PSORT and TargetP. Abbreviated as Subcell.
• TMD - Abbreviation of transmembrane domain.
• Transmembrane domain - The helix structure part of the transmembrane protein. We used the data predicted by two programs such as TMHMM and SOSUI. Abbreviated as TMD.
• UTR - Abbreviation of untranslated region.

Programs

• BLASTZ - Sequence alignment program for whole-genome alignment. The web site is http://www.psc.edu/general/software/packages/blastz/.
• InterProScan - Protein motif sequence search program to InterPro database. The web site is http://www.ebi.ac.uk/InterProScan/.
• RepeatMasker - Detection program of repeat elements like retrotransposon. The web site is http://www.repeatmasker.org/.
• RESCUE-ESE - Prediction program of ESE. The web site is http://genes.mit.edu/burgelab/rescue-ese/.
• SOSUI - Prediction program of transmembrane domain. The web site is http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0.html.
• TargetP - Prediction program of subcellular localization signal. The web site is http://www.cbs.dtu.dk/services/TargetP/.
• TMHMM - Prediction programe of transmembrane domain. The web site is http://www.cbs.dtu.dk/services/TMHMM/.
• WoLF PSORT - Prediction program of subcellular localization signal. Abbreviated as WPSORT. The web site is http://wolfpsort.seq.cbrc.jp/aboutWoLF_PSORT.html.en.