Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcatacttttgtccttgttatcctgtataaggtttcttctttgtttctaactgactccatgctggtacgtgtggaaatctccagGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08930.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
gtaagttcatacttttgtccttgttatcctgtataaggtttcttctttgtttctaactgactccatgctggtacg-tgtggaaatctccagGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC
|| ||| | | ||| ||| | | || || | || | | | || ||| |||||| | || |||||||||||||| |||||||||||||| || || | || || || ||||||| |||||||||||||||||| | || ||||| ||
--------gtatatttctgttcattacattgttctgaactcgtcct--attgatgacagtagcttgaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 9
--------------------------------------gtaagttcatacttttgtccttgttatcctgtataaggtttcttctttgtttctaactgactccatgctggtacgtgtggaaatctccagGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC
|| || | || | | | ||| | | ||| || ||| | |||| ||| | ||| | | || || |||||||| | ||||||||||| ||||| || ||||| ||||||||||| |||||||| || ||||| || |||||||| || ||| || || ||||||||
gtatgttggaaaactcaggctatttttctttccttcagttatgtataataattgatacattatattatatgtaatattctttcaattaatctagatga-tatatg-taatttgttctt---tcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTTTTCATTAC
upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 8
--------gtaagttcatacttttgtccttgttatc----ctgtataa-ggtttcttctttgtttctaac--tgactccat-------gctggtacgtgtggaaatctc------cagGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC
| ||| ||| || || | ||| || ||||||| || | | || | | ||| | | || | | || || ||| || |||||||| | ||||||||||| ||||| || ||||| ||||||||||| |||||||| || ||||| || |||||||| || ||| || || ||||||||
gtatgttggaaagctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgtaatttgttctttcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTTTTCATTAC
upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 9
-------------gtaagttcatacttttgtcctt--gttatcctgtataa--ggtttcttctttgt--ttctaactgactccatgctggt-acgtgtggaaat--------ctccagGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC
| || || || | ||||| ||||| |||| | | || | ||| | | | | | | || | | | | || || | | |||||||| | ||||||||||| ||||| || ||||| ||||||||||| |||||||| || ||||| || |||||||| || ||| || || ||||||||
gtatgttggaaggctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgcaatttgttctttcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTATTCATTAC
upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 9
----------------------------gtaagttcatacttttgtccttgttatcctgtataaggtttcttctttgtttctaactga------ctccatgctgg-tacgtgtggaaatctccagGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC
| | | ||| | || | | | | | | | | ||| || | | | | || |||| || | | | || |||||||| | || || ||||| ||||| || ||||| ||||||||||| |||||||| || ||||| || |||||||| || ||| || || ||||||||
gtatgttggattactcttacctttagtgattattccattaccataagctagagagtatacagacattatatattttaattttcattcagttattcttcatgatgtctgcattctactttcatcagGTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGAGCCATGATGCTTGGGCTGAGACTAGTTTTCATTAC
upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttcatacttttgtccttgttatcctgtataaggtttcttctttgtttctaactgactccatgctggtacgtgt---ggaaatctcc---agGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC
||| ||| ||| ||| | || | | | | || ||| || | ||| ||| || ||| | || | | | ||| | |||||| || || ||||| || ||||| |||||||| ||||||||||| ||||| || || || |||||||||||||| || | | | || ||||||||
gtactgctatagattt----ttgctgtc-tctgttattttatttcctt-tcactagatgatcttattctgagatgtatcttgtacttcttcgtcagGTCTCTTGGGTACTGCAGCATTTGCATTCTTCTGCTTCTACCTTCTGCTTGCGGTGATTGCAGGGGCAATGATGCTTGGACTTAGATTAGTTTTCATTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggtttcttctttgtttctaactgactccatgctggtacgtgtggaaatctccagGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC
tctcc CT-rich tract
tttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcatacttttgtccttgttatcctgtataaggtttcttctttgtttctaactgactccatgctggtacgtgtggaaatctccagGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG