Sequence
atgc intronic sequence ATGC exonic sequencegttttctttgctgcagatttttagaagtgttacactctcttcgcatgagtgtttaatatgtatatacttatctcttttcttttgtagGTTCCTTTTGCACGCTCATCTCTGAATCATGATGATGTGTTTATCTTGGACACCAAGGAAAAGATTTATCAGTTTAATGGTGCAAATTCAAATATCCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G57410.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 5
gttttctttgctgcagatttttagaagtgttacactctcttcgcatgagtgtttaatatgtatatacttatctcttttcttttgtagGTTCCTTTTGCACGCTCATCTCTGAATCATGATGATGTGTTTATCTTGGACACCAAGGAAAAGATTTATCAGTTTAATGGTGCAAATTCAAATATCCAAG
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gtgactactatttcacctccctgtt--tcttagactactttatc-----tcctcatgttatatacactaaatgtcctatattc--agGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 4
-------gttttctttgctgcagatttttagaagtgttacactctcttcgcatgagtgtttaatatgtatatacttatctcttttcttttgtagGTTCCTTTTGCACGCTCATCTCTGAATCATGATGATGTGTTTATCTTGGACACCAAGGAAAAGATTTATCAGTTTAATGGTGCAAATTCAAATATCCAAG
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gcatagtgttctctattcatgtacttttcaaatgcagtgcacattcattgactaaaaatgtgatacaaag----------ttttccttatgcagGTTCCTTTTGCACGGTCTTCACTGAATCATGATGATGTATTCATCCTAGACACTCAGAATAAGATTTATCAATTCAATGGTGCAAACTCCAATATCCAGG
upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 5
-------------gttttctttgctgcagatttttagaagtgttacactctcttcgcatgagtgtttaatatgtatatacttatctcttttcttttgtagGTTCCTTTTGCACGCTCATCTCTGAATCATGATGATGTGTTTATCTTGGACACCAAGGAAAAGATTTATCAGTTTAATGGTGCAAATTCAAATATCCAAG
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gtcagaataaaacaggcacaatgttctctattcatgtacttttcaaattcagtgcacattcgttgcctaaaaatgtg-atacaaagttttgcttatgcagGTCCCTTTTGCACGGTCTTCATTGAATCATGATGATGTATTCATCCTAGACACTCAGAATAAGATTTATCAATTCAATGGTGCAAACTCCAATATCCAGG
upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 4
gttttctttgctgcagatttttagaagtgttacactctcttcgcatg-agtgtttaatatgtatatacttatctcttttcttttgtagGTTCCTTTTGCACGCTCATCTCTGAATCATGATGATGTGTTTATCTTGGACACCAAGGAAAAGATTTATCAGTTTAATGGTGCAAATTCAAATATCCAAG
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gtagtatattctcccaacatgta----tttcatgatctaatcacgttcactgtgctgcagctggtcacctg-cattttggttgtgcagGTCCCCTTTGCTCGGTCTTCACTAAATCACGATGATGTGTTTATCCTGGACACAGAAAATAAAATTTATCAGTTCAATGGTGCAAATTCCAATATCCAGGMapped 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|116482622|gb|EG525214.1|EG525214EST: AAACCCGGCTGTATACCTGCAAAGGAAAACGTGCTGTCCACTTGAAGCAG GTTCCTTTTGCACGCTCATCTCTGAATCATGATGATGTGTTTATCTTGGAC
genomic: AAACCCGGCTGTATACCTGCAAAGGAAAACGTGCTGTCCACTTGAAGCAGgttttctttg ... tcttttgtagGTTCCTTTTGCACGCTCATCTCTGAATCATGATGATGTGTTTATCTTGGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactctcttcgcatgagtgtttaatatgtatatacttatctcttttcttttgtagGTTCCTTTTGCACGCTCATCTCTGAATCATGATGATGTGTTTATCTTGGACACCAAGGAAAAGATTTATCAGTTTAATGGTGCAAATTCAAATATCCAAG
gtttaat putative branch site (score: 4)
tatacttatctctttt putative PPT
tttaatatgtatatac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttctttgctgcagatttttagaagtgttacactctcttcgcatgagtgtttaatatgtatatacttatctcttttcttttgtagGTTCCTTTTGCACGCTCATCTCTGAATCATGATGATGTGTTTATCTTGGACACCAAGGAAAAGATTTATCAGTTTAATGGTGCAAATTCAAATATCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA