Sequence
atgc intronic sequence ATGC exonic sequence...ttagagagtagatagggagggctggatttatgcgcattttcgttgagagttgagtctctcattaatcaagtccctctgtttggtgaattgaacaaatcagGTTCTGTGGTTCCAATGCTTGAAGCCGTGATGGCAGTTGTGCCAGCGGACAAGCTGGCTGTTCACTTCCATGATACCTATGGGCAAGCTCTTGCAAACAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G26800.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G26800.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 6
-----ttagagagtagatagggagggctggatttatgcgcattttcgttgagagttgagtctctcattaatcaagtccctctgtttggtgaattgaacaaatcagGTTCTGTGGTTCCAATGCTTGAAGCCGTGATGGCAGTTGTGCCAGCGGACAAGCTGGCTGTTCACTTCCATGATACCTATGGGCAAGCTCTTGCAAACAT
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ttttctttgtgtattaatccaaaaaa-tgaatattctttattggttactcaaatatgatctttgtattcatattgttt-tctgttcattctgttgtg---gtcagGAACTGTAGTTCCAATGCTTTTGGCTGTAATGGCTGTTGTGCCAGCGGAGAAGCTTGCTGTCCACTTCCATGACACTTACGGGCAATCCCTTGCAAATAT
upper sequence: AT2G26800.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 8
-----ttagagagtagatagggagggctggatttatgcgcattttcgttgagagttgagtctctcattaatcaagtccctctgtttggtgaattgaacaaatcagGTTCTGTGGTTCCAATGCTTGAAGCCGTGATGGCAGTTGTGCCAGCGGACAAGCTGGCTGTTCACTTCCATGATACCTATGGGCAAGCTCTTGCAAACAT
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ttaatccagaatatgaatattctttataaaaactttctat-tggttactcaaatatgatctttgtactcatattgttt-tctgttcattctgttgtg---gtcagGAACTGTAGTTCCAATGCTTTTGGCTGTAATGGCTGTTGTGCCAGCAGAGAAGCTTGCTGTCCACTTCCATGACACTTATGGGCAATCCCTTCCAAATAT
upper sequence: AT2G26800.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 6
-----------ttagagagtagatagggagggctggatttatgcgcattttcgttgagagtt-gagtctctcattaatcaagtccctctgtttggtgaattgaacaaatcagGTTCTGTGGTTCCAATGCTTGAAGCCGTGATGGCAGTTGTGCCAGCGGACAAGCTGGCTGTTCACTTCCATGATACCTATGGGCAAGCTCTTGCAAACAT
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agcttaatgtatttgatagtttgtgtcaataattag--ttaaatgcagtagaattaagaaagagaaaccatcatctataatcttcatttattt----------atgtatcagGCGCCATTGTTCCTATGCTTGAAGCTGTAATGGCTGTTGTTCCTGTTGAGAAGCTTGCTGTCCACTTCCATGACACTTATGGGCAGTCTCTTCCAAATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagttgagtctctcattaatcaagtccctctgtttggtgaattgaacaaatcagGTTCTGTGGTTCCAATGCTTGAAGCCGTGATGGCAGTTGTGCCAGCGGACAAGCTGGCTGTTCACTTCCATGATACCTATGGGCAAGCTCTTGCAAACAT
cattaat putative branch site (score: 3)
attaatcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagagagtagatagggagggctggatttatgcgcattttcgttgagagttgagtctctcattaatcaagtccctctgtttggtgaattgaacaaatcagGTTCTGTGGTTCCAATGCTTGAAGCCGTGATGGCAGTTGTGCCAGCGGACAAGCTGGCTGTTCACTTCCATGATACCTATGGGCAAGCTCTTGCAAACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - tctctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaag