Sequence
atgc intronic sequence ATGC exonic sequencegtacacacattctttttgcaagatatgtctttgctagttccttacttgttctcttaagctctacaacttggttagtgcaaagtttactctactcttatcttgttatgcaagagctgcttaaaattttcttaacttattaatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G32400.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G32400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G33930.1 (Glycine max), 3'ss of exon 6
gtacacacattctttttgcaagatatgtctttgctagttccttacttgttctcttaagctctacaacttggttagtgcaaagtttactctactcttatcttgttatgcaagagctgcttaaaattttcttaacttattaatctttgg-ttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
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-------------------------------------------------aattttaaaccattcaa-ttagtcagaaaggaatgt-ctccaatcgcagagaaacatgccaa---tttataattgtattctcatgtgctaatcattgtctttcagTGTGCTGTGCTTGCATTGGATGATTCAGTATTGGATGTTGATCAAGTTGAGAACCTCATAAAATTCTCTCCAACCAAAGAAGAGATGGAAATGCTGAAG
upper sequence: AT3G32400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g06530.t01 (Vitis vinifera), 3'ss of exon 9
gtacacacattctttttgcaagatatgtctttgctagttccttacttgttctcttaagctctacaacttggttagtg--caaagtttactctactcttatcttgttatgcaagagctgcttaaaattttcttaacttattaatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
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---------------------------------cttgtgtctgttcagcaattctagtcccagacacgtggtaagtaaacagagtctgattagttctt-tctt-tcattctggcttgccttcaaatgtt--------------------ttacagAGCTCAGTCCTTGCCTTGGATGATTCAGCATTAGATGTTGATCAAGTTGATAACCTCATAAAGTTCTGTCCAACAAAAGAAGAGATTGAACTACTCAAG
upper sequence: AT3G32400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ33545 (Selaginella moellendorffii), 3'ss of exon 6
gtacacacattctttttgcaagatatgtctttgctagttccttacttgttctcttaagctctacaacttggttagtgcaaagtttactctactcttatcttgttatgcaagagctgcttaaaattttcttaacttattaatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
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----------------------------------------------------------------------------------------------gtaagttgctctctac--attatgcaatgtggtttttacttccaactct-------cagAAAGCAATACTAGCGTTGGATGGGACGGTACTGGATGTTGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACGAAGGAGGAGATGGAAACGCTCAAG
upper sequence: AT3G32400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ36895 (Selaginella moellendorffii), 3'ss of exon 6
gtacacacattctttttgcaagatatgtctttgctagttccttacttgttctcttaagctctacaacttggttagtgcaaagtttactctactcttatcttgttatgcaagagctgcttaaaattttcttaacttattaatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
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----------------------------------------------------------------------------------------------gtaagttgctctctac--attatgcaatgtggtttttactt-ccaaccct------cagAAAGCAATACTAGCGTTGGATGGGACGGTACTGGATGTTGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACGAAGGAGGAGATGGAAACGCTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgttatgcaagagctgcttaaaattttcttaacttattaatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
tattaat putative branch site (score: 2)
tcttt CT-rich tract
ttaaaattttcttaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacacacattctttttgcaagatatgtctttgctagttccttacttgttctcttaagctctacaacttggttagtgcaaagtttactctactcttatcttgttatgcaagagctgcttaaaattttcttaacttattaatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC