The quest for a more complete genome extends to locating the genomic origins of cDNAs that possess no cognate genomic sequence in the current tiling path.
In order to maintain an up-to-date list of these "missing genes", all cDNAs and ESTs in GenBank are searched periodically against the current version of the genome,
which includes sequences derived from a number of unanchored contig BACs. cDNAs without a genomic alignment are being investigated sytematically to determine
whether they exist in the Columbia ecotype and to identify BACs to which they hybridize. The table below shows our progress to date in identifying a corresponding
genomic region for each cDNA and is updated as these are uncovered. Note that 2% of approximately 180,000 Arabidopsis ESTs do not have a genomic allignment (not shown)
but no experimental investigation has been initiated in these cases.
| Missing Gene |
GenBank Accession |
Ecotype |
PCR'd from Ler |
PCR'd from Col-0 |
Status |
GenBank Comments |
| SKP1-like protein ASK10 (ASK10) |
AF132729 |
Col-0 |
No |
No |
possibly located on BACs T8F15 or T8G18; sequencing in progress |
constructed from non-sterile tissue |
| Rac-like protein |
U88402 |
Col-0 |
No |
No |
unable to PCR from genomic or cDNA |
|
| cab3 promoter-binding protein |
L33781 |
RLD |
No |
No |
unable to PCR from genomic DNA |
|
| flavanol sulfotransferase-like protein |
AJ006409 |
Ler |
No |
No |
unable to PCR from genomic DNA; original cDNA was lost in a fire (J. Milner, personal communication) |
|
| C19H04 |
AF325055 |
Col-0 |
No |
No |
cDNA and PCR product do not hybridize to TAMU & IGF BAC filters |
|
| plant-type connexin 32 |
M63234 |
Col-0 |
No |
No |
highly homologous to AY065403, unable to PCR from genomic DNA |
|
| unknown protein |
BT002460 |
Col-0 |
No |
No |
unable to PCR from genomic DNA |
|
| unknown protein |
BT002485 |
Col-0 |
No |
No |
unable to PCR from genomic DNA |
|
| unknown protein |
BT002491 |
Col-0 |
No |
No |
unable to PCR from genomic DNA |
|
| unknown protein |
BT002503 |
Col-0 |
No |
No |
unable to PCR from genomic DNA |
|
| unknown protein |
BT002525 |
Col-0 |
No |
No |
unable to PCR from genomic DNA |
|
| clone sps372 unknown |
AF083730 |
|
No |
No |
unable to PCR from genomic DNA |
|
| 60S L13 ribosomal protein (diDi 13A-1 gene) |
AJ286347 |
Col-0 |
No |
No |
unable to PCR from genomic DNA |
|
| hypothetical protein (DiDi 14C-2a gene) |
AJ286355 |
Col-0 |
No |
No |
unable to PCR from genomic DNA |
possible source of the sequence is contaminating nematode Meloidogyne incognita |
| hypothetical protein (DiDi 1C-4c gene) |
AJ286352 |
Col-0 |
No |
No |
unable to PCR from genomic DNA |
possible source of the sequence is contaminating nematode Meloidogyne incognita |
| clone DiDi 12C-1a |
AJ276739 |
No |
No |
No |
unable to PCR from genomic DNA |
nematode-induced galls |
| clone DiDi 17C-2a |
AJ276750 |
|
No |
No |
unable to PCR from genomic DNA |
nematode-induced galls |
| partial small nucleolar RNA snoR75 |
AJ505646 |
None |
No |
No |
unable to PCR from genomic DNA |
|
| glutathione transferase |
X68304 |
Ler |
No |
No |
unable to PCR from genomic DNA |
|
| transposon Tag1 putative transposase |
AF051562 |
None |
No |
No |
not in Col-0; PMID:9475754 |
|
| cyclophilin-like protein |
X63616 |
Ler |
No |
No |
contaminating sequence, PMID:9426607 |
|
| peptide transporter (ptr2) |
U01171 |
Ler |
|
No |
contaminating sequence, G. Stacey (personal communication) |
|
| hypothetical protein |
AJ132767 |
None |
|
No |
contaminating sequence, L.G. Josefsson (personal communication) |
|
| UMP/CMP kinase (pyr6) |
AF000147 |
Ler |
|
Yes |
Located on BAC T7I7 |
|
| RAFL04-14-M02 |
AY091157 |
Col-0 |
|
Yes |
Located on BAC F13M11 |
hits ESTs (AI995690, AA394370, AA395071) |
| cytokinin oxidase (CKX5) |
AF303981 |
Col-0 |
|
Yes |
Located on BAC F13M11 |
|
| PnC401 homologue |
AB050965 |
Col-0 |
|
Yes |
Located on BAC F13M11 |
|
| T28A8_100 |
AY050350 |
Col-0 |
|
Yes |
Located on BAC F13M11 |
|
| T28A8_100 (subset of above) |
AY094037 |
Col-0 |
|
Yes |
Located on BAC F13M11 |
|
| RAP 2.9 |
AF003102 |
Ler |
|
No |
Located on BAC F15N16 |
|
| ABA-responsive element binding protein 1 (AREB1) |
AB017160 |
Col-0 |
|
Yes |
Located on BAC T2P3 |
|
| RFX5 |
AB008025 |
Col-0 |
|
Yes |
Located on BAC T7A14 |
|
| 2 abscisic acid responsive elements-binding factor (ABRE) |
AF093545 |
Col-0 |
|
Yes |
Located on BAC T2P3 |
|
Page last updated: 30 July 2003.
