Sequence
atgc intronic sequence ATGC exonic sequencegtgactgtactgttagctctctcattagatgtgttgctatctcgaatcgggaaactgatgcagaagaaatatgtatagTTTCCTTGTAGCAATGGGAGACATATCTCTGAGGAAGACTGGAGTGGAAGAGAAGAGGGCTAAAGCACAGAAGGAGTCCAATGCTCTTCTTGACTATACA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G41350.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G41350.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0049g01470.t01 (Vitis vinifera), 3'ss of exon 2
---------------------gtgactgtactgttagctctctcattagatgtgttgctatctcgaatcgggaaactgatgcagaagaa-atatgtat--agTTTCCTTGTAGCAATGGGAGACATATCTCTGAGGAAGACTGGAGTGGAAGAGAAGAGGGCTAAAGCACAGAAGGAGTCCAATGCTCTTCTTGACTATACA
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gtcggttgggtttgtgttaatattccattaccgatgttccttttttttttttcccctgcttttaggattttgagttttatataaagggagatgtggatttagTTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGAGAAGAGGGCTAAAGTGCAGAAGGAGTCCAAAATTCTTCTTGATTACACC
upper sequence: AT2G41350.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0073g00670.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------gtgactg-tactgttagctctc-tcattagatgtgttgctatctcgaatcgggaaactgatgcagaagaaatatgtat--agTTTCCTTGTAGCAATGGGAGACATATCTCTGAGGAAGACTGGAGTGGAAGAGAAGAGGGCTAAAGCACAGAAGGAGTCCAATGCTCTTCTTGACTATACA
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gtgggttgggtttttgttaatattccattaccgatgttctttattattattattttttttcctgcttttaggattttgggttttatatgaggggagatgtggattcagTTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAATCTGAAGTGGAGGAGAAGAGGGCTAAAGTGCAGAAGGAGTCCAAAATTCTTCTTGATTACACCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|125011986|gb|EL084255.1|EL084255EST: CTTGCAAATGTGGCTAATTTGTTGAACATACGGGACACTGAACTGAGCAG TTTCCTTGTAGCAATGGGAGACATATCTCTGAGGAAGA
genomic: CTTGCAAATGTGGCTAATTTGTTGAACATACGGGACACTGAACTGAGCAGgtgactgtac ... atatgtatagTTTCCTTGTAGCAATGGGAGACATATCTCTGAGGAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagatgtgttgctatctcgaatcgggaaactgatgcagaagaaatatgtatagTTTCCTTGTAGCAATGGGAGACATATCTCTGAGGAAGACTGGAGTGGAAGAGAAGAGGGCTAAAGCACAGAAGGAGTCCAATGCTCTTCTTGACTATACA
aactgat putative branch site (score: 3)
aagaaatatgtata TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgactgtactgttagctctctcattagatgtgttgctatctcgaatcgggaaactgatgcagaagaaatatgtatagTTTCCTTGTAGCAATGGGAGACATATCTCTGAGGAAGACTGGAGTGGAAGAGAAGAGGGCTAAAGCACAGAAGGAGTCCAATGCTCTTCTTGACTATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG