Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatagaaaacatgatagtatgatactgaagcttattatagatacttcacaacatattttgaagcaaaatgatcttaccttttactattcaatatagAAACACAGCATCTGAAACCGTCAAGCAAAAGCTGGTTTTTGCTGGAAGTGAAGAAGGGAAACTTCTTGCTCTTCGCCAAAGCTTTGCAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G09720.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G09720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os07g45360.1 (Oryza sativa), 3'ss of exon 7
gtaagtatagaaaacatgatagtatgatactgaagcttattatagatacttcacaacatattttgaagcaaaatgatcttaccttttactattca-atatagAAACACAGCATCTGAAACCGTCAAGCAAAAGCTGGTTTTTGCTGGAAGTGAAGAAGGGAAACTTCTTGCTCTTCGCCAAAGCTTTGCAGAG
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---------------------gtaag-tattgct-ttcacagtgtgtactgcgaaaactattttttca-gggttatttttgtcattaattcttcacatacagGAATTCAGCCTCTTCACTGATTAAGCAAAAGTTGATTTTCGCTGGAACTGAGAAGGGGAAGTTGCTAGCTCTTCGCCAAAGCTTTGCAGAA
upper sequence: AT3G09720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA19G36300.1 (Glycine max), 3'ss of exon 8
gtaagt-----atagaaaacatgatagtatgatactg--aagcttattatagatacttcacaacatattttgaagcaaaatgatcttacc---ttttactattcaatatagAAACACAGCATCTGAAACCGTCAAGCAAAAGCTGGTTTTTGCTGGAAGTGAAGAAGGGAAACTTCTTGCTCTTCGCCAAAGCTTTGCAGAG
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gtaagtttgctgcaaaacatttacaaacatggtgctcctgagcatattgttagttaat-acagttttcttcacattattttgttgatgcccaatgcttttatgcgcatcagGAATATGGCTTCTGAAACAATAAAGCAAAAATTGGTTTTTACTGGAAGTGAAGAAGGAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAG
upper sequence: AT3G09720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G33590.1 (Glycine max), 3'ss of exon 8
gtaagt-----atagaaaacatgatagtatgatactg--aagcttattatagatacttcacaacatattttgaagca---aaatgatcttaccttttactattcaatatagAAACACAGCATCTGAAACCGTCAAGCAAAAGCTGGTTTTTGCTGGAAGTGAAGAAGGGAAACTTCTTGCTCTTCGCCAAAGCTTTGCAGAG
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gtaagtttgttgcaaaacatttacaaacatggtgctcctaagcattttgttagttaat-acagttttcttcacattatttagttgatgtctaattcttttatgtgcatcagGAATATGGCTTCTGAAACAATAAAGCAAAAATTGGTTTTTACTGGAAGTGAAGAAGGAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAG
upper sequence: AT3G09720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0040g02300.t01 (Vitis vinifera), 3'ss of exon 8
-gtaagtatagaaaacatgatagtatgatactgaagcttattatagatacttcacaacatattttgaagcaaaatgatcttaccttttactattcaatatagAAACACAGCATCTGAAACCGTCAAGCAAAAGCTGGTTTTTGCTGGAAGTGAAGAAGGGAAACTTCTTGCTCTTCGCCAAAGCTTTGCAGAG
| || ||| | | | || || | || | | ||| ||||| || | | | ||| | || | | || || | || |||||| | |||||||| ||||| ||||||||||||||||| ||||| |||||||||||||| |||||||||||||||
taatggaatggaatggttttgatgaatattcttccacaatttttgcaggctttgtt-tgcattttattattaattcagtgctcatttgaaattttga-acagGAATTCTGCTTCTGAACTTATAAAGCAAAAACTGGTGTTTGCTGGAAGTGAAGAGGGGAAGCTTCTTGCTCTTCGTCAAAGCTTTGCAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacttcacaacatattttgaagcaaaatgatcttaccttttactattcaatatagAAACACAGCATCTGAAACCGTCAAGCAAAAGCTGGTTTTTGCTGGAAGTGAAGAAGGGAAACTTCTTGCTCTTCGCCAAAGCTTTGCAGAG
atcttac putative branch site (score: 3)
ttttactattcaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatagaaaacatgatagtatgatactgaagcttattatagatacttcacaacatattttgaagcaaaatgatcttaccttttactattcaatatagAAACACAGCATCTGAAACCGTCAAGCAAAAGCTGGTTTTTGCTGGAAGTGAAGAAGGGAAACTTCTTGCTCTTCGCCAAAGCTTTGCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG