Sequence
atgc intronic sequence ATGC exonic sequence...cttcatgtttttgttgtgaatattccgtgaggatttatatctctgtcgattggctggtaaacactgtattactgattgaactgggatggtatttttttagTATGGTCGTGAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGGCGAATGACTTCAAAGATCGAGAAGCCGCGTCTGCTAATCCTTGGAGGAGCTCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G33240.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G33240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g34950.1 (Oryza sativa), 3'ss of exon 2
---cttcatgtttttg-ttgtgaatattccgtgaggatttatatctctgtcgattggctggtaaacactgtat-tactgattgaactgggatggtatttttttagTATGGTCGTGAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGGCGAATGACTTCAAAGATCGAGAAGCCGCGTCTGCTAATCCTTGGAGGAGCTCTG
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ttttatcaagttattggcctttgaaatttcacac---tttattactttttcg--tatcttattagtgctccatgtaagagcttcattttggttctttatttccagTTTTGTTGTAAAAGGAGTTGTTTGTAAGAAGAATGTTGCTCATCGGCGCATGGCGTCACGGAAAGAAAAGCCACGCATCCTGATCCTTGGTGGTGCACTT
upper sequence: AT4G33240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G153722_T01 (Zea mays), 3'ss of exon 2
----cttcatgtttttgttgtgaatattccgtgaggatttatatctctgtcgattggctggtaaacactgtattactgattgaactgggatggtatttttttagTATGGTCGTGAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGGCGAATGACTTCAAAGATCGAGAAGCCGCGTCTGCTAATCCTTGGAGGAGCTCTG
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gatctattacgttttgagtttca-tactgtatttatctgtgcatttctttggttt---ccaccagttcttttttttggttttatacatcttcctttatttgcagTTTCGTTGTAAAAGGAGTTGTTTGTAAGAAGAATGTTGCTCACCGGCGTATGTCATCAAAAAAGGAAAAGCCTCCAATCTTGATTCTTGGTGGTGCACTC
upper sequence: AT4G33240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G05000.1 (Glycine max), 3'ss of exon 5
cttcatgtttttgttgtgaatattccgtgaggatttatatctctgtcgattggctggtaaacactgtattactgattgaactgggatggtattttttta------gTATGGTCGTGAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGGCGAATGACTTCAAAGATCGAGAAGCCGCGTCTGCTAATCCTTGGAGGAGCTCTG
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-ttcatatgattgttgt---tttgcaagaagtctttataagtttgttcgttatctgttctat-ctgtctctgt-atagtcttgatgttctagttttctatgtccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGCGGTGCTTTG
upper sequence: AT4G33240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G17510.1 (Glycine max), 3'ss of exon 2
cttcatgtttttgttgtgaatattccgtgaggatttatatctctgtcgattggctggtaaacactgtattac-tgattgaactgggatggtatt---tttttagTATGGTCGTGAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGGCGAATGACTTCAAAGATCGAGAAGCCGCGTCTGCTAATCCTTGGAGGAGCTCTG
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-tccatatgattgtcgt---tctgggagaagtctttataagtttgttcattatgtgttctatctgtccctgtatggtcttgatgttttagttttttatttccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGAGGTGCTTTG
upper sequence: AT4G33240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0016g00360.t01 (Vitis vinifera), 3'ss of exon 2
---cttcatgtttttgttgtgaatattccgtgaggatttatatctctgtcgattggctggtaaacactgtattactgattgaactgggatggtat-ttttttagTATGGTCGTGAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGGCGAATGACTTCAAAGATCGAGAAGCCGCGTCTGCTAATCCTTGGAGGAGCTCTG
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acaattgacaatcaccttgcaaacacttta----actagaggatgctgtcaatttctttttctttttctttgtactgatgaaattttaatttcatatcttccagTATGGTGGTTAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGACGAATGACATCTAAAATAAGTAAACCACGTTTCCTACTCCTCGGAGGAGCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgattggctggtaaacactgtattactgattgaactgggatggtatttttttagTATGGTCGTGAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGGCGAATGACTTCAAAGATCGAGAAGCCGCGTCTGCTAATCCTTGGAGGAGCTCTG
tactgat putative branch site (score: 2)
tattttttt putative PPT
atggtattttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcatgtttttgttgtgaatattccgtgaggatttatatctctgtcgattggctggtaaacactgtattactgattgaactgggatggtatttttttagTATGGTCGTGAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGGCGAATGACTTCAAAGATCGAGAAGCCGCGTCTGCTAATCCTTGGAGGAGCTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT