Sequence
atgc intronic sequence ATGC exonic sequencegtatcatttttttcttctttcttattttgtataaccaagaaatatcatttcctgaaaggattataaatacacgttgaacagtgtcttttatgatttataacaacacgacaatcggacaatgtacagGAGGACTTTGGAGGGGGCCACCCGGATCCCAATCTTACCTATGCTAAGGAGCTCGTGGCACGCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G70730.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 9
gtatcatttttttcttctttcttattttgtataaccaagaaatatcatttcctgaaaggattataaatacacgttgaacagtgtcttttatgatttataacaacacgacaatcggacaatgtacagGAGGACTTTGGAGGGGGCCACCCGGATCCCAATCTTACCTATGCTAAGGAGCTCGTGGCACGCATGGGATTGAGTAAAACTGATGATGCTGG-TGGCGAGC
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--------------------------------------gtaatttgttttctt-------ctatcatcacaatttgaa-aatagaattta-gattggtgttcattctttacttgtatttt-tacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAAATCCTCAAATGCTGAACCCCCAG-
upper sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 9
gtatcatttttttcttctttcttattttgtataaccaagaaatatcatttcctgaaaggattataaatacacgttgaacagtgtcttttatgatttataacaacacgacaatcggacaatgtacagGAGGACTTTGGAGGGGGCCACCCGGATCCCAATCTTACCTATGCTAAGGAGCTCGTGGCACGCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGC------
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-----------------------------------------gtaatgagttcttctattgtcacaaatatctactta-taatgtggctaggtattaatt-catcacttatatt------tttgcaggagGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGG--AAAGTCATCCT-CAAATGTTGAGCCTCCTG
upper sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 9
gtatcatttttttcttctttcttattttgtataaccaagaaatatcatttcctgaaaggattataaatacacgttgaacagtgtcttttatgatttataacaacacgacaatcggacaatgtacagGAGGACTTTGGAGGGGGCCACCCGGATCCCAATCTTACCTATGCTAAGGAGCTCGTGGCACGCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGC---
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-----------------------------------------gtaatgagttcttctattgtcacaaatatctactta-taatgtggctaggtattaatt-catcacttatatt------tttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGG--AAAGTCATCCT-CAAATGTTGAGCCTC
upper sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
gtatcatttttttcttctttcttattttgtataaccaagaaatatcatttcctgaaaggattataaatacacgttgaacagtgtcttttatgatttataacaacacgacaatcggacaatgtacagGAGGACTTTGGAGGGGGCCACCCGGATCCCAATCTTACCTATGCTAAGGAGCTCGTGGCACGCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGC
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gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaa--ctgaataatttcaaaaccta--------agaatcttttgttatttctttttttg-gctgatttcatg-caaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC
upper sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 8
gtatcatttttttcttctttcttattttgtataaccaagaaatatcatttcctgaaaggattataaatacacgttgaacagtgtcttttatgatttataacaacacgacaatcggacaatgt--acagGAGGACTTTGGAGGGGGCCACCCGGATCCCAATCTTACCTATGCTAAGGAGCTCGTGGCACGCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGC
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--------------------------------------------------------------------------------gtttgtgtttttctttcttcctgttctatacttcaacgttttctacagGAGGACTTTGGTGGAGGCCATCCGGATCCCAATCTCACGTACGCAAAAGAGCTTGTTTTGCGCATGGGACTGGGGAAGACCGGCCCTCCTGCCGATCCAC
upper sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ09195 (Selaginella moellendorffii), 3'ss of exon 8
gtatcatttttttcttctttcttattttgtataaccaagaaatatcatttcctgaaaggattataaatacacgttgaacagtgtcttttatgatttataacaacacgacaatcggacaatgt--acagGAGGACTTTGGAGGGGGCCACCCGGATCCCAATCTTACCTATGCTAAGGAGCTCGTGGCACGCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGC
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--------------------------------------------------------------------------------gtttgtgtttttctttctttctgtgccatacttgaacgttttctacagGAGGACTTTGGCGGAGGCCATCCGGATCCCAATCTCACGTACGCAAAAGAGCTTGTTTTGCGCATGGGACTGGGGAAGACCGGCCCTCCTGCCGATCCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgttgaacagtgtcttttatgatttataacaacacgacaatcggacaatgtacagGAGGACTTTGGAGGGGGCCACCCGGATCCCAATCTTACCTATGCTAAGGAGCTCGTGGCACGCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGC
ttataac putative branch site (score: 2)
ttttatgatttataac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcatttttttcttctttcttattttgtataaccaagaaatatcatttcctgaaaggattataaatacacgttgaacagtgtcttttatgatttataacaacacgacaatcggacaatgtacagGAGGACTTTGGAGGGGGCCACCCGGATCCCAATCTTACCTATGCTAAGGAGCTCGTGGCACGCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG