Table 2 |
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|
Classification and nomenclature of B. pendula PR-10 sequences from our cultivars and GenBank. Indicated are the subfamily (I to V), gene designations (PR-10.01A to PR-10.05), allergen designation if the genes are known to be pollen expressed (Bet v 1.01A to Bet v 1.02C), and allele names as defined in Figure 2. Known isoforms [19] are shown, followed, between brackets, by the GenBank accession number. The tissue of origin is shown in case of mRNA-derived GenBank sequences (L = leaves, R = roots, P = pollen). |
||||||
|
Sub-family |
Gene |
Allergen |
Allele (GenBank no.)*1 |
Known isoforms (GenBank no.)*1 |
Location of transcription |
Sequence identity to reference sequence*2 |
|
|
||||||
|
I |
PR-10.01A |
Bet v 1.01A |
Bet v 1.01A01.01*3 (DQ296566) |
P, P |
100% |
|
|
Bet v 1.01A02.01 (DQ296567) |
- |
99.1% |
||||
|
Bet v 1.01A03.01 (DQ296568) |
- |
99.1% |
||||
|
Bet v 1.1501 (Z72429) |
- |
99.8% |
||||
|
Bet v 1.1502 (Z72432) |
- |
99.8% |
||||
|
Bet v 1.0102 (Z80098) |
P |
99.8% |
||||
|
Bet v 1.0103 (Z80099) |
P |
99.8% |
||||
|
Bet v 1.2501 (Z80101) |
P |
98.8% |
||||
|
Bet v 1.2801 (Z80104) |
P |
99.5% |
||||
|
Bet v 1.3001 (Z80106) |
P |
99.8% |
||||
|
- (AF124838) |
- |
98.6% |
||||
|
- (AJ002107) |
P |
99.8% |
||||
|
- (AJ002109) |
P |
99.3% |
||||
|
- (AJ006905) |
P |
99.8% *4 |
||||
|
- (AJ006911) |
P |
98.6% |
||||
|
- (AJ006913) |
P |
99.5% *4 |
||||
|
|
||||||
|
PR-10.01B |
Bet v 1.01B |
Bet v 1.01B01.01 (DQ296569) |
P, P |
100% |
||
|
Bet v 1d = Bet v 1.0401 (X77266) |
P |
99.3% |
||||
|
Bet v 1h = Bet v 1.0402 (X77270) |
P |
99.8% |
||||
|
- (AJ001551) |
P |
99.8% |
||||
|
|
||||||
|
PR-10.01C |
Bet v 1.01C |
Bet v 1.01C01.01 (DQ296570) |
- |
100% |
||
|
Bet v 1.01C02.01 (DQ296571) |
- |
99.8% |
||||
|
Bet v 1f = Bet v 1.0601 (X77268) |
P |
99.8% |
||||
|
Bet v 1i = Bet v 1.0602 (X77274) |
P |
99.8% |
||||
|
- (AJ001557) |
P |
99.5% |
||||
|
|
||||||
|
PR-10.01D |
Bet v 1.01D |
Bet v 1.01D01.01 (DQ296572) |
- (AJ001555) |
P |
100% |
|
|
Bet v 1.01D02.01 (DQ296573) |
- |
99.1% |
||||
|
Bet v 1.1701 (Z72430) |
- |
98.4% |
||||
|
- (AF124839) |
- |
98.4% |
||||
|
|
||||||
|
II |
PR-10.02A |
Bet v 1.02A |
Bet v 1.02A01.01 (DQ296574) |
- |
100% |
|
|
Bet v 1.02A02.01 (DQ296575) |
- |
99.8% |
||||
|
- (AJ001554) |
P |
99.8% |
||||
|
- (AJ001556) |
P |
99.8% |
||||
|
|
||||||
|
PR-10.02B |
Bet v 1.02B |
Bet v 1.02B01.01 (DQ296576) |
- |
100% |
||
|
Bet v 1.02B02.01a*5 (DQ296577) |
- |
99.3% |
||||
|
Bet v 1.02B02.01b (DQ296578) |
- |
99.3% |
||||
|
Bet v 1.1801 (Z72431) |
- |
99.1% |
||||
|
|
||||||
|
PR-10.02C |
Bet v 1.02C |
Bet v 1.02C02.01 (DQ296580) |
Bet v 1k = Bet v 1.0901 (X77272) |
P |
100% |
|
|
Bet v 1.02C02.02 (DQ296581) |
- |
99.8% |
||||
|
Bet v 1.02C01.01 (DQ296579) |
- |
99.8% |
||||
|
Bet v 1.20101 (Z72434) |
- |
99.3% |
||||
|
Bet v 1c = Bet v 1.0301 (X77265) |
P |
99.8% |
||||
|
Bet v 1.1901 (Z72433) |
- |
98.6% |
||||
|
Bet v 1m = Bet v 1.1401 (X81972) |
P |
99.3% |
||||
|
Bet v 1n = Bet v 1.1402 (X82028) |
P |
99.3% |
||||
|
|
||||||
|
III |
PR-10.03A |
- |
PR-10.03A01.01 (DQ296582) |
- |
100% |
|
|
PR-10.03A02.01 (DQ296583) |
- |
99.8% |
||||
|
|
||||||
|
PR-10.03B |
- |
PR-10.03B01.01 (DQ296584) |
- |
100% |
||
|
PR-10.03B-p01*5 (DQ296586) |
- |
100%*4 |
||||
|
|
||||||
|
PR-10.03B*6 |
PR-10.03B02.01 (DQ296585) |
- |
96.5% |
|||
|
|
||||||
|
PR-10.03C |
- |
PR-10.03C01.01 (DQ296587) |
- (AJ289771) |
- |
100% |
|
|
PR-10.03C02.01 (DQ296588) |
- |
99.5% |
||||
|
PR-10.03C02.02 (DQ296589) |
- |
99.3% |
||||
|
Bet v 1.1201 (X77600) |
L, R |
99.5% |
||||
|
|
||||||
|
PR-10.03D |
- |
PR-10.03D01.01 (DQ296590) |
- |
100% |
||
|
PR-10.03D02.01 (DQ296591) |
- |
99.8% |
||||
|
Bet v 1.1101 (X77599) |
L, R |
99.5% |
||||
|
|
||||||
|
IV |
PR-10.04 |
- |
PR-10.0401.01 (DQ296592) |
- |
100% |
|
|
PR-10.0402.01 (DQ296593) |
- |
98.9% |
||||
|
|
||||||
|
V |
PR-10.05 |
- |
PR-10.0501.03 (DQ296596) |
L, R |
100% |
|
|
PR-10.0501.02 (DQ296595) |
- |
99.5% |
||||
|
PR-10.0501.01 (DQ296594) |
- |
99.8% |
||||
|
PR-10.0501.04 (DQ296597) |
- |
99.8% |
||||
|
PR-10.0502.01 (DQ296598) |
- |
99.8% |
||||
|
|
||||||
|
*1 The known mRNA-derived GenBank sequences contain no intron, while the new gDNA sequences do, aiding in the gene identification. *2 The upper most allele was taken as a reference sequence, identities are calculated for an aligned stretch of 425 bp from base 28 to 452 of the consensus. *3 The last two numerals indicate silent mutations (see Results section for further explanation of the nomenclature) *4 These sequences contain an indel; Sequence identity is calculated excluding the indel. *5 Pseudogene allele. *6In vivo recombination. |
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|
Schenk et al. BMC Genomics 2006 7:168 doi:10.1186/1471-2164-7-168 |
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