Sequence
atgc intronic sequence ATGC exonic sequencegtaatctttattttgagcttatagtaaatcaagcaattagtagaaaattttcctgcagttgatgacgttgcatttggaaaatactgaaaacgctctttggtcctgatgccttttgtttgttccatttactattttatgcagATGGATTCTTCTTGAGGTTCTTGACAAGGTCTCTCCCAGTTCAGTCAACTGGAAGCATGCTTCCAAACCACCGATTAAGATGCCGTTTAGAAAAGTAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26700.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26700.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G556845_T01 (Zea mays), 3'ss of exon 9
gtaatctttattttgagcttatagtaaatcaagcaattagtagaaaattttcctgcagttgatgacgttgcatttggaaaatactgaaaacgctctttggtcctgatgccttttgtttgttccatttactattttatgcagATGGATTCTTCTTGAGGTTCTTGACAAGGTCTCTCCCAGTTCAGTCAACTGGAAGCATGCTTCCAAACCACCGATTAAGATGCCGTTTAGAAAAGTAGAG
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-------------------------------------------------------------gtaa-gacacatttgtagcaaa---aaaaatttttttggt----atatatgttgctacctcaccggagtggtatttgcagATGGGTTTTGCTAGAGGTTCTTGACAAAATTTCTCCAGGGTCAGTTAACTGGAAGCATGCATCCAAACCACCAATCATTATGCCGTTTAGAAAGGTTGAA
upper sequence: AT4G26700.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 9
gtaatctttattttgagcttatagtaaatcaagcaattagtagaaaattttcctgcagttgatgac-gttgcatttggaaaatactgaaaacgctctttggtcctgatgccttttgtttgttc-catttactattttatgcagATGGATTCTTCTTGAGGTTCTTGACAAGGTCTCTCCCAGTTCAGTCAACTGGAAGCATGCTTCCAAACCACCGATTAAGATGCCGTTTAGAAAAGTAGAG
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-----------------------------------------aaataatttt--tgaattggaaagcagaaacaattttatggaacttgatattttgcaagcttttccctagctttcttgatccatagtttctcatgtatgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaacgctctttggtcctgatgccttttgtttgttccatttactattttatgcagATGGATTCTTCTTGAGGTTCTTGACAAGGTCTCTCCCAGTTCAGTCAACTGGAAGCATGCTTCCAAACCACCGATTAAGATGCCGTTTAGAAAAGTAGAG
tcctgat putative branch site (score: 3)
ctatttt putative PPT
atttactattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctttattttgagcttatagtaaatcaagcaattagtagaaaattttcctgcagttgatgacgttgcatttggaaaatactgaaaacgctctttggtcctgatgccttttgtttgttccatttactattttatgcagATGGATTCTTCTTGAGGTTCTTGACAAGGTCTCTCCCAGTTCAGTCAACTGGAAGCATGCTTCCAAACCACCGATTAAGATGCCGTTTAGAAAAGTAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG