Sequence
atgc intronic sequence ATGC exonic sequencegtagattttctgtttatggcatatgtaaatgagaaaataataattttcagtacgtcatataaatgatacgctaaccacattcttataatcgtatctatcgtattatcatttacattgacgtatgtaacactaacttatgtaccttatattggtttcagGTTTTCTACATGGATTCCCTAAAATTCTACCTCTCCTTATATGGCCACAAGTTGCCTGTGATGTGCATTGACATCTCATCAGATGGAGAGTTGATTGTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21540.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G37050.1 (Glycine max), 3'ss of exon 3
gtagattttctgtttatggcatatgtaaatgagaaaataataattttcagtacgtcatataaatgatacgctaaccacattcttataatcgtatctatcgtattatcatttacattgacgtatgtaacactaacttatgt----accttatattggtttcagGTTTTCTACATGGATTCCCTAAAATTCTACCTCTCCTTATATGGCCACAAGTTGCCTGTGATGTGCATTGACATCTCATCAGATGGAGAGTTGATTGTTA
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------------------------------------------------------------cgattttgcactatgagcttgtggtcactcatgtttat-gcattagc-cctattttactatttcaagcattttttttcattataatttcattcatttttcagGTTCACTTTGCAGACACATTCAAATTCTTCCTTTCATTATATGGCCACAAGCTGCCTGTTCTGTGTATGGATATCTCATCAGATGGAGATTTAATTGTAA
upper sequence: AT3G21540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G34360.1 (Glycine max), 3'ss of exon 5
gtagattttctgtttatggcatatgtaaatgagaaaataataattttcagtacgtcatataaatgatacgctaaccacattcttataatcgtatctatcgtattatcatttacattgacgtatgtaacactaacttatgtaccttatattggtttcagGTTTTCTACATGGATTCCCTAAAATTCTACCTCTCCTTATATGGCCACAAGTTGCCTGTGATGTGCATTGACATCTCATCAGATGGAGAGTTGATTGTTA
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--------------------------------------------------------ttgacaattttgtgctatgagcttctggttgttcatttatgcattagccctattt-tactatttcaagtattttttaattata-atttttttcatttttcagGTTCACTTTGCAGACACATTCAAATTCTTCCTTTCATTATATGGCCACAAGCTGCCTGTTCTGTGTATGGATATCTCCTCAGATGGAGATTTAATTGTAA
upper sequence: AT3G21540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g04690.t01 (Vitis vinifera), 3'ss of exon 4
gtagattttctgtttatggcatatgtaaatgagaaaataataattttcagtacgtcatataaatgatacgctaaccacattcttataatcgtatctatcgtattatcatttacattgacgtatgtaacactaacttatgtaccttatattggtttcagGTTTTCTACATGGATTCCCTAAAATTCTACCTCTCCTTATATGGCCACAAGTTGCCTGTGATGTGCATTGACATCTCATCAGATGGAGAGTTGATTGTTA
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-----------------------------------------atgtttcagtgggccaaactgtt--taatataaaagtact---------gcaactattgctttgaaatttcaggtaactgttttgacac--atttatgtcaatcattt----tccagGTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAGCTGCCTGTGCTATGCATGGATGTTTCATCAGATGGAGATTTGCTTGTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcatttacattgacgtatgtaacactaacttatgtaccttatattggtttcagGTTTTCTACATGGATTCCCTAAAATTCTACCTCTCCTTATATGGCCACAAGTTGCCTGTGATGTGCATTGACATCTCATCAGATGGAGAGTTGATTGTTA
cactaac putative branch site (score: 1)
ttatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagattttctgtttatggcatatgtaaatgagaaaataataattttcagtacgtcatataaatgatacgctaaccacattcttataatcgtatctatcgtattatcatttacattgacgtatgtaacactaacttatgtaccttatattggtttcagGTTTTCTACATGGATTCCCTAAAATTCTACCTCTCCTTATATGGCCACAAGTTGCCTGTGATGTGCATTGACATCTCATCAGATGGAGAGTTGATTGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA