Sequence
atgc intronic sequence ATGC exonic sequencegtttgttcagccatgctaaatttctgtttaaacgctctatacactccaatgctgtatgtatacttttcagttattgtctaaaggtactcccttttatgattttagGTACTACCAACAATTGTCAAGCTTTTTGCTTCCAATGATCGAGCTATCAGAGTTTCTCTTTTGCAACATGTTGATCAATTTGGAGAATCAATGTCTGGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G40730.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 10
gtttgttcagccatgctaaatttctgtttaa-acgctctatacactccaatgctgtatgtatacttttcagttattgtctaaaggtactcccttttatgattttagGTACTACCAACAATTGTCAAGCTTTTTGCTTCCAATGATCGAGCTATCAGAGTTTCTCTTTTGCAACATGTTGATCAATTTGGAGAATCAATGTCTGGGC
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gtttgacttcatttctttcgttttcacccaatattcgttagtcattccagtaa---atgtgtgttacgatgttataacacaa-gttaaaaccactggcattttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGAGTTAGCCTTTTGCAGCACATAGATCAGTTTGGGGAGTCATTGACAGCTC
upper sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G098078_T04 (Zea mays), 3'ss of exon 10
gtttgttcagccatgctaaatttctgtttaaacgctctatacactccaatgctgtatgtatacttttcagttatt--gtctaa-aggtactcccttttatgattttagGTACTACCAACAATTGTCAAGCTTTTTGCTTCCAATGATCGAGCTATCAGAGTTTCTCTTTTGCAACATGTTGATCAATTTGGAGAATCAATGTCTGGGC
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---------------gtgacattttctcta----cttattgcgatt-aacactgcttatgaattatcaagtaatctgatataatagagaatgccggctct--tttcagGTCTTGCCAACTATTGTCAAGCTTTTTGCCTCCAATGACCGAGCTATCCGAGCATGTCTTTTGCACCACATAGATCAGTTTGGGGAATCAATGTCTGCTC
upper sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 10
gtttgttcagccatgctaaatttctgtttaaacgctctatacactccaatgctgtatgtatacttttcagttattgtctaaaggtactcccttttatgattttagGTACTACCAACAATTGTCAAGCTTTTTGCTTCCAATGATCGAGCTATCAGAGTTTCTCTTTTGCAACATGTTGATCAATTTGGAGAATCAATGTCTGGGC
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---------------gtgaccttttctcta----cttattatggtt-aatactgcttatgagctatcaagtagtctgattattagagaatgctggcccttttcagGTCTTGCCAACTATTGTCAAGCTTTTTGCCTCCAATGACCGAGCTATCCGAGCATGTCTTTTGCATCACATAAATCAGTTTGGGGAATCAATGTCAGCTC
upper sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G47590.1 (Glycine max), 3'ss of exon 10
-------------------gtttgt-tcagccatgctaaatttctgtttaaacgctctatacactccaatgctgtatgtatacttttcagttattgtctaaaggtactcccttttatgattt-------------tagGTACTACCAACAATTGTCAAGCTTTTTGCTTCCAATGATCGAGCTATCAGAGTTTCTCTTTTGCAACATGTTGATCAATTTGGAGAATCAATGTCTGGGC
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gtaagttataatttcatactttcatgccaatgattttcttttccctttcatacagtgcatac-ttttattgccattt-tactctttttaattaggattcagtcccattcttttattggatttcaatattcatatctagGTACTTCCAACAATTGTAAAACTCTTTGCCTCCAATGATCGAGCTATACGAGTTGCCCTTCTTCAACATATTGATCAATATGGAGAGTCTTTATCAGCGC
upper sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 10
-------------------gtttgt-tcagccatgctaaatttctgtttaaacgctctataca-----ctccaatgctgtatgtatactt----ttcagtt--attgtctaaaggtactcccttttatgattttagGTACTACCAACAATTGTCAAGCTTTTTGCTTCCAATGATCGAGCTATCAGAGTTTCTCTTTTGCAACATGTTGATCAATTTGGAGAATCAATGTCTGGGC
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gtaagttataatttcatacttttatgccaatgattttcttttcccttccatacagtgcatacttttatctccattttactctttataattaggattcagtcccattcttttattggatttcaatattcatatctagGTACTTCCAACAATTGTAAAACTCTTTGCCTCCAATGATCGAGCTATACGAGTTGCCCTTCTTCAACATATTGATCAATATGGAGAGTCGTTATCAGCGC
upper sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 10
----------gtttgttcagccatgctaaatttctgtttaaacgctctatacac----tccaatgctgtatgtatacttttcagttattgtc-taaaggtactcccttttatgattttagGTACTACCAACAATTGTCAAGCTTTTTGCTTCCAATGATCGAGCTATCAGAGTTTCTCTTTTGCAACATGTTGATCAATTTGGAGAATCAATGTCTGGGC
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gtgtataacaacttcaacacctttatgatgccccttttctactttctttcatacggtgcttgattctctctctctaaccaggatttcttctcatgcttgtattggatttcactatat-agGTGCTTCCAACAATTGTTAAACTTTTTGCATCCAATGACCGAGCTATTCGAGTTGGCCTTCTTCAACATATTGATCAGTTTGGGGAGTCATTATCAGCACMapped 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|86065920|gb|DR361677.1|DR361677EST: CCTTACTTAAGATGGGTTCGTGGTTATCAACTGAAGATTTCAGTGTCAAG GTACTACCAACAATTGTCAAGCTTTTTGCTTCCA
genomic: CCTTACTTAAGATGGGTTCGTGGTTATCAACTGAAGATTTCAGTGTCAAGgtttgttcag ... atgattttagGTACTACCAACAATTGTCAAGCTTTTTGCTTCCA
EST:
gi|125165280|gb|EL191635.1|EL191635EST: CCTTACTTAAGATGGGTTCGTGGTTATCAACTGAAGATTTCAGTGTCAAG GTACTACCAACAATTGTCAAGTCTTTTTGCTTCCAATGATCGAGCTATCAG
genomic: CCTTACTTAAGATGGGTTCGTGGTTATCAACTGAAGATTTCAGTGTCAAGgtttgttcag ... atgattttagGTACTACCAACAATTGTCAAG-CTTTTTGCTTCCAATGATCGAGCTATCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgtatgtatacttttcagttattgtctaaaggtactcccttttatgattttagGTACTACCAACAATTGTCAAGCTTTTTGCTTCCAATGATCGAGCTATCAGAGTTTCTCTTTTGCAACATGTTGATCAATTTGGAGAATCAATGTCTGGGC
gtctaaa putative branch site (score: 3)
ctcccttttat putative PPT
ttttatgatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttcagccatgctaaatttctgtttaaacgctctatacactccaatgctgtatgtatacttttcagttattgtctaaaggtactcccttttatgattttagGTACTACCAACAATTGTCAAGCTTTTTGCTTCCAATGATCGAGCTATCAGAGTTTCTCTTTTGCAACATGTTGATCAATTTGGAGAATCAATGTCTGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA