Kazusa Clone (Original Type)
Description of the Gene/Protein Characteristic Table
Features of the cloned DNA sequence
This section describes features of the nucleotide sequences of
cDNA clones actually characterized. Although the actual clones
contained an oligo(dT)-NotI adapter primer sequence and a SalI adapter
sequence at their 3'- and 5'-extremities, respectively, the nucleotide
sequences of these adapters are not shown here. This section is
intended to provide clone users with detailed information of clones,
which is not available from the public databases.
(1) Physical map
- The physical maps were constructed on the basis of the
sequence data of the cDNA clones. The horizontal scale
represents the cDNA length in kb. The ORFs and untranslated regions
are shown by solid and open boxes, respectively. The positions of
the first ATG codons are indicated by solid and open triangles
to indicate respectively those that lie within and outside
the confines of Kozak's rule. RepeatMasker, which is a program
that screens DNA sequences for interspersed repeats known to
exist in mammalian genomes, was applied to detect repeat sequences
in cDNA sequences (Smit, A. F. A. and Green, P.,
). Alu sequences and other
repetitive sequences detected in this way are displayed
by dotted and hatched boxes, respectively.
(2) Restriction map
- Commercially available restriction enzymes
Roberts, R. J., Macelis, D.
"REBASE - restriction enzymes and methylases"
Nucleic Acids Res. 1998; 26: 338-350).
) are sorted according
to the number of the restriction sites present in the cDNA insert.
(3) Prediction of the protein coding region (GeneMark analysis)
- The graphic outputs of the GeneMark-RC analysis are displayed. Vertical
lines given in the graphs indicate the positions of termination codons.
If you would like to know more about the GeneMark-RC analysis,
please read the paper by Hirosawa et al.
(Hirosawa, M., Isono, K., Hayes, W., Borodovsky, M.
"Gene identification and classification in the Synechocystis genomic
sequence by recursive gene mark analysis" DNA Seq. 1997;
The GeneMark analysis gives the following warnings:
(a) Warning for N-terminal truncation of the coding region;
(b) Warning for spurious interruption of the coding region.
(4) Prediction of the genomic structure of the cDNA
- The cDNA sequence was subjected to BLAST search
(Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z.,
Miller, W., and Lipman, D.J.
Gapped BLAST and PSI-BLAST: a new generation of protein database
search programs." 1997; Nucleic Acids Res 25: 3389-3402)
the human genome draft sequences in NCBI.
When a genomic fragment was found to be considerably similar to the cDNA
sequence (E-value = 0.0 and sequence identity is 90% or greater), the genomic
structure of the cDNA was assigned by
(Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., and Miller, W. "
A computer program for aligning a cDNA sequence with a genomic DNA sequence
1998; Genome Res. 8: 967-974)
on the genomic fragment.
Features of the predicted protein sequence
This section describes the features of the predicted protein sequence.
(1) Revision of the cloned DNA sequence before prediction of the protein
- When necessary, the cDNA sequences of the isolated clones were
revised by direct RT-PCR/sequencing experiments in order to eliminate
artifact(s) signaled by the GeneMark-RC analysis (see "Features
of the cloned DNA sequence"). Therefore, some of the predicted
protein sequences are not derived from the cloned cDNA sequence
but from the revised cDNA sequence. Hence, it should be noted
that some cDNA clones do not carry the identical sequences to those
deposited to GenBank/EMBL/DDBJ databases because they are the
experimentally revised ones. To avoid any confusion, this section
states whether or not the predicted protein sequence is obtained
by conceptual translation of the revised cDNA sequence.
The revised sequences by the RT-PCR/sequencing experiments can be
accessible by clicking. As far as possible, the nature of the revision
is also described (deletion, insertion, nonsense mutation, or
removal of retianed intronic sequence).
(2) FASTA homology searches against the nr database
- Top 5 entries given the expectation value smaller than 0.001 in nr
database are shown.
"nr" stands for the non-redundant amino acid sequence database
that has been constructed by NCBI.
The numbers on the left and right
sides of a black line in the graphical overview indicate the lengths
(in amino acid residues) of the non-homologous N-terminal and
C-terminal portions flanking the homologous region (indicated by the
black line), respectively. The FASTA output and the multiple alignment
of these entries can be obtained by clicking.
(3) Analysis of Motifs, Domains, and Membrane-spanning regions
The predicted protein sequences were examined for motifs present
in the InterPro database.
Because weakly defined sequence motifs appear too many times in
general and are, thus, unlikely to be informative,
the following motifs were excluded from the
analysis: amidation site; N-glycosylation site; cAMP- and
cGMP-dependent protein kinase phosphorylation site; casein kinase II
phosphorylation site; N-myristoylation site; protein kinase C
phosphorylation site; and tyrosine kinase phosphorylation site.
Motifs/Domains in the InterPro database were searched for by InterProScan. (Zdobnov, EM, and Apweiler, R. InterProScan--an integration platform for the signature-recognition methods in InterPro" Bioinformatics 2001; 17:847-848).
Membrane-spanning region were predicted by
(Hirokawa, T., Boon-Chieng, S., Mitaku, S.
"SOSUI: classification and
secondary structure prediction system for membrane proteins"
Bioinformatics 1998; 14:378-379).