Sequence
atgc intronic sequence ATGC exonic sequencegttagttctgttacagcagagcagtatgtgaatctctgtcaagtgtctgttgttgatcgtttattctcctgaactgctgcagGTGGTGGAAGCTGGTGGACTTCACGTGGTGGGGACAGAGCGGCATGAATCACGTCGAATAGACAATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01800.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM5G880102_T01 (Zea mays), 3'ss of exon 2
gtta-gttctgttacagcagagcagtatgtgaatct--ctgtcaagtgtc--tgttgttgatcgtttattctcctgaactgctgcagGTGGTGGAAGCTGGTGGACTTCACGTGGTGGGGACAGAGCGGCATGAATCACGTCGAATAGACAATCAG
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gttatatggcattataaaagaaacattgatagctctatctgttgctgttcagtgtagcgtagtgttcacgtgatcaattttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA02G01060.2 (Glycine max), 3'ss of exon 14
gttagttctgttacagcagagcagtatgtgaatctctgtcaagtgtctgttgttg-atcgtttattctcctgaactgctgcagGTGGTGGAAGCTGGTGGACTTCACGTGGTGGGGACAGAGCGGCATGAATCACGTCGAATAGACAATCAG
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gtcaatt-tgtttc--ttgactaatactt---cccttcatacattgctgttgatgcattattaatgatcatta-tgactgcagGTTGTGGAAGCTGGTGGACTACATGTAGTAGGCACAGAGCGTCATGAATCACGTCGAATTGATAATCAG
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 14
gttagttctgttacagcagagcagtatgtgaatctctgtcaagtgtctgttgttg-atcgtttattctcctgaactgctgcagGTGGTGGAAGCTGGTGGACTTCACGTGGTGGGGACAGAGCGGCATGAATCACGTCGAATAGACAATCAG
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gtcaatt-tgtttc--ttgactagtactt---cccctcatacattgctgttgatacattattaatgatcatta-tgactgcagGTTGTGGAAGCTGGCGGACTACATGTAGTAGGCACAGAGCGTCATGAATCACGTCGAATTGATAATCAG
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 14
gttagttctgtta-cagcagagcagtatg--tgaatctctgtcaa---gtgtctgttgttgatcgtttattctcctgaactgctgcagGTGGTGGAAGCTGGTGGACTTCACGTGGTGGGGACAGAGCGGCATGAATCACGTCGAATAGACAATCAG
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gttagttcaattttccaaacaccagtttgaacggaaggttgtcaatttatataaactgt-aatttctgttatttctacattcctacagGTTGTGTCAGCAGGTGGACTTCATGTGGTGGGGACAGAACGGCATGAATCTCGTCGAATTGACAATCAGMapped 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|164076232|gb|ES112269.1|ES112269EST: TGGCGATAGCGAAAGAATATAAGGGCTACACTGATGAAGAAAGGAAGAAG GTGGTGGAAGCTGGTGGACTTCACGTGGTGGGGACAGAGCGGCAT
genomic: TGGCGATAGCGAAAGAATATAAGGGCTACACTGATGAAGAAAGGAAGAAGgttagttctg ... actgctgcagGTGGTGGAAGCTGGTGGACTTCACGTGGTGGGGACAGAGCGGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaatctctgtcaagtgtctgttgttgatcgtttattctcctgaactgctgcagGTGGTGGAAGCTGGTGGACTTCACGTGGTGGGGACAGAGCGGCATGAATCACGTCGAATAGACAATCAG
tgttgat putative branch site (score: 4)
tttattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttctgttacagcagagcagtatgtgaatctctgtcaagtgtctgttgttgatcgtttattctcctgaactgctgcagGTGGTGGAAGCTGGTGGACTTCACGTGGTGGGGACAGAGCGGCATGAATCACGTCGAATAGACAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG