Sequence
atgc intronic sequence ATGC exonic sequence...gtataaatcttaaggagctcacacaaagaaattgttgtctaaaagagaatgtgtcagtgcagaatagctttacttacacagttttcttgtatatggatagGATGATACTGCTTTCGAGAAACAGAGTGCTCTTTTTGCACTTGCAGTCTCAGACATAGTTCTTATAAACAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13870.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 4
-gtataaatcttaaggagctcacacaaagaaattgttgtctaaaaga-gaatgtgtcagtgcagaatagctttacttacacagttttcttgtatatggat-agGATGATACTGCTTTCGAGAAACAGAGTGCTCTTTTTGCACTTGCAGTCTCAGACATAGTTCTTATAAACAT
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catgctattctctgtcattggcaaaaattagaacaaagtatgagaaatggatatttctgcgtt---tcgttctccttgtatagtgaaattgtctttttctcagGATGACACTGCTTTTGAAAAGCAGAGTGCTCTATTTGCTCTTGCTGTCTCAGATATAGTGCTAATAAACAT
upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 4
gtataaatcttaaggagctcacacaaagaaattgttgtctaaaagagaatgtgtcagtgca-gaatagctttacttacacagttttcttgtatatggat-agGATGATACTGCTTTCGAGAAACAGAGTGCTCTTTTTGCACTTGCAGTCTCAGACATAGTTCTTATAAACAT
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-aacatgtcattctctg-tcattggcaaaaattagaacagtatgagaaatggatagttttgcgttttgttctccttgtatactgaaattgtctttttctcagGATGACACTGCTTTTGAAAAGCAGAGTGCTCTATTTGCTCTTGCTGTCTCAGATATAGTGCTAATAAACAT
upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 4
gtataaatcttaaggagctcacacaaagaaattgttgtctaaaagagaatgtgtcagtgc-agaatagctt-tacttacacagtt--ttcttg-tatatggatagGATGATACTGCTTTCGAGAAACAGAGTGCTCTTTTTGCACTTGCAGTCTCAGACATAGTTCTTATAAACAT
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---ttgatctttacatgattttg--atctgtctagactaagaaggaaaatggattacttttagcacttcttgcaacctaatatttggtttttgctttcttgtcagGATGATACTGCATTTGAGAAGCAGAGTGCCCTTTTTGCTCTTGCTGTTTCAGACATAGTGCTAATCAACATMapped 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|116444534|gb|EG487126.1|EG487126EST: GCACCGTTGTGATGGATTTAGAGGGTACCGATGGGAGAGAGCGTGGTGAG GATGATACTGCTTTCGAGAAACAGAGTGCTCTTTTTGCACTTGCAGTCTCA
genomic: GCACCGTTGTGATGGATTTAGAGGGTACCGATGGGAGAGAGCGTGGTGAGgtgtgtaacc ... atatggatagGATGATACTGCTTTCGAGAAACAGAGTGCTCTTTTTGCACTTGCAGTCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaatgtgtcagtgcagaatagctttacttacacagttttcttgtatatggatagGATGATACTGCTTTCGAGAAACAGAGTGCTCTTTTTGCACTTGCAGTCTCAGACATAGTTCTTATAAACAT
tacttac putative branch site (score: 1)
tttactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataaatcttaaggagctcacacaaagaaattgttgtctaaaagagaatgtgtcagtgcagaatagctttacttacacagttttcttgtatatggatagGATGATACTGCTTTCGAGAAACAGAGTGCTCTTTTTGCACTTGCAGTCTCAGACATAGTTCTTATAAACAT
- - - - - - - - - - acacaaa
- - - - - - - - - - - - - - - - - - - ctaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttaca