Sequence
atgc intronic sequence ATGC exonic sequencegtagcttaatgacctcgtttctcatttctagatatgatgaacatattgcatctactgtgaaggaatgaagaacagaaatgctccatcaagattatactgtttttgttttgcccaattttctaatggtatttttgacagGCCATACTGGCGATGCTATTTCCCGAATACACAAGCAGTGATCTATGTTGTTGACTCGAGTGATACAGATAGAATCGGGGTGGCGAAAGAGGAGTTTCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G24765.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G24765.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0052g01720.t01 (Vitis vinifera), 3'ss of exon 5
gtagcttaatgacctcgtttctcatttctagatatgatgaacatattgcatctactgtgaaggaatgaagaacagaaatgctccatcaagattatactgtttttgttttgcccaattttctaatggtatttttg-acagGCCATACTGGCGATGCTATTTCCCGAATACACAAGCAGTGATCTATGTTGTTGACTCGAGTGATACAGATAGAATCGGGGTGGCGAAAGAGGAGTTTCAT
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----------------------------------caatgtttcaatt-tacctttcttttgggcata---atttgtaagtttgcatcaagggcacaggatcatcagct-gcttgtttggtttatgttttttgggcacagGCCATATTGGAGATGCTATTTTCCAAATACTCAAGCCATAATATATGTTGTTGATTCAAGTGATACTGATAGATTGGTAATAGCTAAAGATGAGTTTCAT
upper sequence: AT2G24765.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0008g07360.t01 (Vitis vinifera), 3'ss of exon 4
gtagcttaatgacctcgtttctcatttctagatatgatgaacatattgcatctactgtgaagga-atgaagaacagaaatgctc-catcaagattatactgtttttgttttgcccaattttctaatggt-----atttt-tgacagGCCATACTGGCGATGCTATTTCCCGAATACACAAGCAGTGATCTATGTTGTTGACTCGAGTGATACAGATAGAATCGGGGTGGCGAAAGAGGAGTTTCAT
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---------------------------------------------ctgt-tgttctgtgaagcttatagattattatgctgattgctttaaggttattatctctgcaattcattggctcatcaactgtttcttcattttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGTTGACTCAAGTGACACTGATAGAATTGTAATAGCCAAGGATGAATTTCAT
upper sequence: AT2G24765.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S78_17V6.1 (Physcomitrella patens), 3'ss of exon 4
gtagcttaatgacctcgtttctcatttctagatatgatgaacatattg-catctactgtgaaggaatgaagaacagaaatgctccatcaagattatactgtttttgttttgcccaattttctaatggtatttttgacagGCCATACTGGCGATGCTATTTCCCGAATACACAAGCAGTGATCTATGTTGTTGACTCGAGTGATACAGATAGAATCGGGGTGGCGAAAGAGGAGTTTCAT
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gtaacttatttaactc----ccgaattcaggttggaatttctattttgatgaatgatttctatgaattgtgactctgacttccgaatgaa--tcaaatcgt-------------aattttgtttgggaaatttttgcagACCTTATTGGCGATGCTATTACCCAAACACACAAGCAATCATCTACGTGGTAGACTCCAGTGATACAGAACGCATGTCCACGGCTCAAGATGAGTTTCATMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86084655|gb|DR380414.1|DR380414EST: ATTTAGGTGGACAAACAAGCATCAG GCCATACTGGCGATGCTATTTCCCGAATACACAAGCAGTGATCTATGTTGT
genomic: ATTTAGGTGGACAAACAAGCATCAGgtagcttaat ... tttttgacagGCCATACTGGCGATGCTATTTCCCGAATACACAAGCAGTGATCTATGTTGT
EST:
gi|124933836|gb|EL010958.1|EL010958EST: ATTTAGGTGGACAAACAAGCATCAG GCCATACTGGCGATGCTATTTCCCGAATACACAGGCAGTGATCTAT
genomic: ATTTAGGTGGACAAACAAGCATCAGgtagcttaat ... tttttgacagGCCATACTGGCGATGCTATTTCCCGAATACACAAGCAGTGATCTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcaagattatactgtttttgttttgcccaattttctaatggtatttttgacagGCCATACTGGCGATGCTATTTCCCGAATACACAAGCAGTGATCTATGTTGTTGACTCGAGTGATACAGATAGAATCGGGGTGGCGAAAGAGGAGTTTCAT
ttctaat putative branch site (score: 2)
tattttt putative PPT
attatactgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcttaatgacctcgtttctcatttctagatatgatgaacatattgcatctactgtgaaggaatgaagaacagaaatgctccatcaagattatactgtttttgttttgcccaattttctaatggtatttttgacagGCCATACTGGCGATGCTATTTCCCGAATACACAAGCAGTGATCTATGTTGTTGACTCGAGTGATACAGATAGAATCGGGGTGGCGAAAGAGGAGTTTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG