Sequence
atgc intronic sequence ATGC exonic sequencegtttggataaattatactctgaactatatcaatagatgacagaacttgaagggttttcgttcgttgaagtaacataaaaaccctgattttctcttgtttctttgcagTATATGGCTCTAATTGGCAGTCGTGGTCACCGAGAAGAGCTAATAGAGCTTATAAATCAAAAAGAGGTTGTTGGGGATCTCTTTAACCAACTTCGGCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G48960.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G21240.1 (Glycine max), 3'ss of exon 11
gtttggataaattatactctgaactatatcaatagatgacagaacttgaagggttttcgttcgttgaagtaacataaaaaccctgattttctcttgtttctttgcagTATATGGCTCTAATTGGCAGTCGTGGTCACCGAGAAGAGCTAATAGAGCTTATAAATCAAAAAGAGGTTGTTGGGGATCTCTTTAACCAACTTCGGCTTG
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attttg-caaaccata---tgtactgtgttgagcaactattctactttaactgatctgcaaagctgaaaacttctttgtgcttt-ataaaatgttaaaaatt--cagTACACTGCCCTAATTCGTAGCCGGGGTCGTAGACAATCATTGGTAGAGCTTATCAATCAAAAGGAGGTTGTTGTTGATCTCTTTAACCAACTGCGGCTGG
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 12
----gtttggataaattatactctgaactatatcaatagatgacagaacttgaagggttttcgttcgttgaagtaacataaaaaccctgattttctcttgtttct-ttgcagTATATGGCTCTAATTGGCAGTCGTGGTCACCGAGAAGAGCTAATAGAGCTTATAAATCAAAAAGAGGTTGTTGGGGATCTCTTTAACCAACTTCGGCTTG
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gttagtacaatcagtttatgtt-tgactcatgtttctgagtaaagaaaaattccagaacttaatttttctccttg------------tgctttgtaaatgttcaaactgcagTACAGTGCCTTGATTGGTAGCCGTGGTTATAGAGAATCATTGGTGGAGCTTATTAGTCAAAAGGAGGTTGTAGGGGATCTCTTTAATCAACTTCGGCTGG
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 12
gtttggataaattatactctgaactatat-caatagatgacagaacttgaagggttttcgttcgttgaagtaacataaaaaccctgattttctcttgtttct-ttgcagTATATGGCTCTAATTGGCAGTCGTGGTCACCGAGAAGAGCTAATAGAGCTTATAAATCAAAAAGAGGTTGTTGGGGATCTCTTTAACCAACTTCGGCTTG
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---tgaactgcatgta-tcagtactatttatagcaaatatgatgccatgacaggatccagcc-----atgtaataatatccttgtgctttgtaaatgttcaaactgcagTACGATGCCTTGATTGGTAGCCGCAGTTATAGAGAATCATTGGTGGAGCTTATTAATCAAAAGGAGATTGTAGGGGATCTCTTTAATCAACTTCGGCTGG
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 12
gtttggataaattatactctgaactatatcaatagatgacagaacttgaagggttttcgttcgttgaa-gtaacataaaaaccctgattttctcttgtttctttg------cagTATATGGCTCTAATTGGCAGTCGTGGTCACCGAGAAGAGCTAATAGAGCTTATAAATCAAAAAGAGGTTGTTGGGGATCTCTTTAACCAACTTCGGCTTG
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------------tatatttgaaa--atgatattttctttcatatttttaacattctcaactgattaaatgctgaaaatggtcccttttcatgtgttattaatttggaaatgcagTATAATGCATTGATTCGTAGTAGCAGTCATCGGGCCACACTGATAGACCTTATAAATCAGAAGGAAGTTGTAGGAGATCTATTTAACCAACTTCGACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttcgttcgttgaagtaacataaaaaccctgattttctcttgtttctttgcagTATATGGCTCTAATTGGCAGTCGTGGTCACCGAGAAGAGCTAATAGAGCTTATAAATCAAAAAGAGGTTGTTGGGGATCTCTTTAACCAACTTCGGCTTG
ccctgattttctcttg CT-rich tract
aagtaacataaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggataaattatactctgaactatatcaatagatgacagaacttgaagggttttcgttcgttgaagtaacataaaaaccctgattttctcttgtttctttgcagTATATGGCTCTAATTGGCAGTCGTGGTCACCGAGAAGAGCTAATAGAGCTTATAAATCAAAAAGAGGTTGTTGGGGATCTCTTTAACCAACTTCGGCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG