Sequence
atgc intronic sequence ATGC exonic sequencegttaagtcttgcaaacttctgttctagacaacatcattctttgtctatgtacacacacagatgcatatacttattacgcatcttagataattgacttttagtctttcaatttcagAGGAAATGGTATCGCAACTTTCTGATGAAGGGTTTCCATCTTGTGGTTCTATTAGCTGCTGGTCCTGGTATTCGGGATACACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39630.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g60700.1 (Oryza sativa), 3'ss of exon 8
gttaagtcttgcaaacttctgttctagacaacatcattctttgtctatgtacacacacagatgcatatacttattacgcatcttagataattgacttttagtctttcaatttcagAGGAAATGGTATCGCAACTTTCTGATGAAGGGTTTCCATCTTGTGGTTCTATTAGCTGCTGGTCCTGGTATTCGGGATACACAG
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-gtaagtgccccccacccca-----aaacaaaaaaccttttcaatcgtgcgtttttgttctcttagattttcatgttgtgttgtatttgtgcttttcctggcgt----actgcagAGGAAATGGTATCGGAATTTTCTTATGAAAGGTTTCCACCTGGTAGTTTTATTGACAGCTGGTCCTGGGATCAGAGACACACAG
upper sequence: AT2G39630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G129620_T01 (Zea mays), 3'ss of exon 8
gttaagtcttgcaaacttctgttctagacaacatcattctttgtctatgtacacacacagatgcatatacttattacgcatcttagataattgacttttagtctttcaatttcagAGGAAATGGTATCGCAACTTTCTGATGAAGGGTTTCCATCTTGTGGTTCTATTAGCTGCTGGTCCTGGTATTCGGGATACACAG
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----------gtaattctctttactgctcactacccttggtcttttggttttctactaagtt-------ttcaccttgcatttttctt--tttcctatcctgcttt--attgcagAGGAAATGGTATAGAAACTTTCTTATGAAAGGTTTCCATTTGGTAGTTTTGTTGACTGCTGGTCCCGGGATCAAAGATACACAG
upper sequence: AT2G39630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G52810.1 (Glycine max), 3'ss of exon 8
gttaagtcttgcaaacttctgttctagacaacatcattctttgtctatgtacacacacagatgcatatacttattacgcatcttagataattgacttttagtctttcaatttcagAGGAAATGGTATCGCAACTTTCTGATGAAGGGTTTCCATCTTGTGGTTCTATTAGCTGCTGGTCCTGGTATTCGGGATACACAG-
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-----------------ttaagtgtggccttcttcattctttgttt---------tattgttgc-catatgtttagatcatcttggttgaataacttaaattaatgc--tttcagaGGAAGTGGTACCGCAATTTTTTGATGAAGGGCTTCCATCTTGTGGTTCTCTTGGCTGCTGGTCCTGGAATTCGTGATACACAGG
upper sequence: AT2G39630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G10150.1 (Glycine max), 3'ss of exon 8
gttaagtcttgcaaacttctgttctagacaacatcattctttgtctatgtacacacacagatgcatatacttattacgcatcttagataattgacttttagtctttcaatttcagAGGAAATGGTATCGCAACTTTCTGATGAAGGGTTTCCATCTTGTGGTTCTATTAGCTGCTGGTCCTGGTATTCGGGATACACAG
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---------------gttatgtgtt-gccttcttcattctttgttttattgttgccatatgtgtagat----------catcttggttgaataacttaaattgatgc--tttcagAGGAAGTGGTACCGCAATTTTTTGATGAAGGGCTTCCATCTTGTGGTTCTCATGGCTGCTGGTCCTGGAATTTGTGATACACAG
upper sequence: AT2G39630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv13s0019g01230.t01 (Vitis vinifera), 3'ss of exon 8
gttaagtcttgcaaacttctgttctagacaacatcattctttgtctatgtacacacacagatgcatatacttattacgcatcttagataattgacttttagtctttcaatttcagAGGAAATGGTATCGCAACTTTCTGATGAAGGGTTTCCATCTTGTGGTTCTATTAGCTGCTGGTCCTGGTATTCGGGATACACAG
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----------------gttgagtcttgctgatgacgtttgct-tctttatatattttcgattttttata-ttgttaa--atttttcttagtagagtta----cttcatttttcagAGGAAGTGGTACCGCAATTTTTTAATGAAGGGTTTCCATGTTGTGGTTCTCTTAACTGCTGGTCCTGGAATTCGGGATACACAGMapped 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|86076734|gb|DR372491.1|DR372491EST: TATCCGCATTTGGTTCTCGTGCTCATCTCGAGGAGAAAGCTCTTGCTACA AGGAAATGGTATCGCAACTTTCTGATGAAGGGTTTCCATCTTGTGGTTCTA
genomic: TATCCGCATTTGGTTCTCGTGCTCATCTCGAGGAGAAAGCTCTTGCTACAgttaagtctt ... tcaatttcagAGGAAATGGTATCGCAACTTTCTGATGAAGGGTTTCCATCTTGTGGTTCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcatatacttattacgcatcttagataattgacttttagtctttcaatttcagAGGAAATGGTATCGCAACTTTCTGATGAAGGGTTTCCATCTTGTGGTTCTATTAGCTGCTGGTCCTGGTATTCGGGATACACAG
aattgac putative branch site (score: 3)
tctttc putative PPT
ataattgactttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaagtcttgcaaacttctgttctagacaacatcattctttgtctatgtacacacacagatgcatatacttattacgcatcttagataattgacttttagtctttcaatttcagAGGAAATGGTATCGCAACTTTCTGATGAAGGGTTTCCATCTTGTGGTTCTATTAGCTGCTGGTCCTGGTATTCGGGATACACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT