Table 1 |
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U12 type of introns identified in T. spiralis. |
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|
EST |
Genomic sequence |
Intron length |
B |
R |
Relationship to C. elegans |
C. elegans orthologue |
Gene function |
|
ATAC introns |
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|
|
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EX501652.1 |
AGA|ATATCCTTTC...TTGGGCATTGTTATATTTCCTTAACGGGTATGGTTTAC|GTT |
2095 |
+ |
+ |
U12->U2 |
EEED8.7 |
SR (splicing factor) |
|
TyrIleGl nPheGlnGl nLeuLysAspAla |
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|
Ts TACATAGAAT...ACGTTCGAAGA GCTGAAAGATGCT |
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|
PheValAr gPheTyrGl nArgArgAspAla |
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|
Ce TTCGTTAG ATTTTATGAGT...AGACGTCGTGCTGCT |
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|
EX500683.1 |
ATT|ATATCCTTTC...AATTTCATTTCCTTAACGTTAGATTTTTGTTGTTTTAC|TGA |
94 |
+ |
+ |
U12 lost |
E04D5.1a |
NA |
|
ES570647.1 |
ATC|ATATCCTTTC...GTATTGTTTGTATTTTCCTTAACTTCATATGTTTTTAC|GTA |
182 |
+ |
+ |
U12 lost |
Y37D8A.10 |
Signal peptidase complex, subunit SPC25 |
|
|
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GTAG introns |
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|
|
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|
EX499999.1 |
Ts GAG|GTATCCTTTG...TTTTGTTTTTCTCTCTTTTTACAATTATTATACAG|GCC |
90 |
- |
+ |
U12->U2 |
F10F2.1 |
PH, BEACH and WD40 domain-containing protein |
|
Ce GAG|GTTTGAAACA...TTTTAATATTGAACTAAAATTTTTGAATTTTCCAG|GCG |
64 |
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|
ES570692.1 |
Ts TAG|GTATTGTTTT...TGCTACAAGGAATTTTTTTATTGCTTTGATTTTAG|AGT |
617 |
- |
- |
U12->U2 |
F40F8.10 |
Small ribosomal subunit S9 protein |
|
Ce CCG|GTTTAGTTTT...AAGATTAGTATCGACTTCAAATTCTTCTCTTTCAG|TGT |
291 |
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|
ES561213.1 |
Ts TCG|GTATTATTTT...CATATTAATCGTTTCATTTCTTAATGTATTTTTAG|TGG |
54 |
- |
- |
U12->U2 |
ZC395.10 |
NA |
|
Ce CCA|GTACGTTTCG...ACATAGAATGAGTCGTAATTCGTAAATTTTCAGAG|GAA |
150 |
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|
EX500486.1 |
Ts TCG|GTATTCTTTC...TAATATGTTTTTCTTTTTTTTCAACTTATTTTAAG|ATT |
87 |
- |
+ |
U12->U2 |
ZC328.3a |
NA |
|
Ce CAT|GTGAGTTTCA...TCCTGAATTTATTCAAGTTTCAACCACATTTCCAG|CAT |
758 |
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|
ES569928.1 |
ATG|GTATTCTTTT...ATTTCCATTACAAAATTACAACCGCGTTGTTCTTTCAG|TGC |
107 |
+ |
+ |
Not known |
Y82E9BR.15 |
Transcription elongation factor B |
|
ES565768.1 |
CAG|GTATTCTTTT...CAAATTTTGGAAAAATTCTTTTTTTTTAATCCGAACAG|GTA |
94 |
- |
+ |
Not known |
C34D4.4a |
NA |
|
ES562099.1 |
AAT|GTATCCTTAA...TGTATGAGGTTTGGTATTTCTGATTTTAATCATTTTAG|TGT |
50 |
- |
+ |
Not known |
R07E5.14 |
RRM RNA binding domain) containing |
|
ES563059.1 |
GCG|GTATCTTTTC...TATTTATAACTGAATCGTTTTTATTAATAATTTTTTAG|AGT |
54 |
- |
+ |
Not known |
M04F3.4 |
NA |
|
BQ738460.1 |
ACG|GTATCGTTCA...TCAATTTTTTTAAAAGTAATTTTCTTCATATATTTTAG|AAC |
72 |
- |
- |
U12 lost/Not known |
Y56A3A.36 |
NA |
|
ES566079.1 |
TGG|GTATCGTTCG...ATTAACTAACACTTTGAAGTTGACAAGTGAATGTTTAG|GAT |
140 |
- |
- |
Not known |
M02B7.4 |
beta-1,4-N-acetylglucosaminyl transferase |
|
EX500543.1 |
TCG|GTATTCTTTG...TTATTATTAATTTCTGTTTTTTTTGGTTTTCTAAACAG|AGA |
86 |
- |
+ |
None |
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|
ES561535.1 |
GGG|GTATTATTTT...TTTTCTGTGATTTAATTGCATTTTAATGTTCTATCTAG|TGA |
71 |
- |
- |
None |
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|
BQ738918.1 |
GAA|GTATCTTTTA...TGAATTTTGCTAAATTGTACTTAACAGGTTGTTTTTAG|AAA |
153 |
- |
+ |
None |
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|
|
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|
Table shows all introns identified by the Sheth et al method [11]. Regions with best match to branch site PWM is underlined. For one of the ATAC introns (EST EX501652.1) is shown the shift in 5' splice site observed between T. spiralis and C. elegans. Rule of 5' splice site (R) is that 5' splice site sequence is RTATCCTT where one of the Cs in positions +5 and +6 may be converted into a T. Burge et al method (B) is described in [5]. NA = not available. For sequences of U2 and U12 introns listed in table, see additional file 2. |
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Bartschat and Samuelsson BMC Genomics 2010 11:106 doi:10.1186/1471-2164-11-106 |
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