Sequence
atgc intronic sequence ATGC exonic sequencegtgcgatgattctatctcgaatgtgtttttacttttgaactcttactctcttttgcatttcaattcatatgcacaccaaaccattaactaatttcttgagcctagctcaattagatcttgtaaagtttattttcttgatgcataacagtcttattcgtcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G34560.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 6
gtgcgatgattctatctcgaatgtgtttttacttttgaactcttactctcttttgcatttcaattcatatgcacacca-aaccattaactaatttcttgagcctagctcaattagatcttgtaaagtttattttcttgatgcataacagtcttattcgtcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG
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------------------------------------------------------------------atatttgcattgtgagtactttgaaattttctgattttgcaatatctctgtctattactatatacttcggtagtcagtttcaagca-attcctatt-tgcagACAATGCTGGCAAAGGCTGTTGCTACTGAGTGTAAAACTACATTCTTCAACATTTCAGCATCATCAATTGTTAGCAAATGGCGTG
upper sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g48270.1 (Oryza sativa), 3'ss of exon 6
gtgcgatgattctatctcgaatgtgtttttacttttgaactcttactctcttttgcatttcaattcatatgcacaccaaaccattaactaatttcttgagcctagctcaattagatcttgtaaagtttattttcttgatgcataacagtctt-attcgtcttgtg-cagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG
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-----------------------------------------------------------------caactccgtttccattccatatgttgcttgtcgtgctatacgaactcaaat--tgctgatcatgtatgcttgatg--taactgttttgatatattttgtttcagACAATGCTAGCAAAAGCTGTGGCTACTGAGTGCAAAACAACCTTCTTCAATATTTCAGCCTCATCAATTGTCAGTAAATGGCGTG
upper sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 6
gtgcgatgattctatctcgaatgtgtttttacttttgaactcttactctcttttgcatttcaattcatatgcacaccaaaccattaactaatttcttgagcctagctcaattagatct-tgtaaagtttattttcttgatgcataacagtcttattcgtcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG
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-------------------------------------------------------------ggttcagagtcactatta--tgttgagcatttggtatattctcatgcacttatccctgtacaaagacatgcctctcagttt-taactg----gatcctgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG
upper sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 6
gtgcgatgattctatctcgaatgtgtttttacttttgaactcttactctcttttgcatttcaattcatatgcacaccaaaccattaactaatttcttgagcctagctcaattagatcttgtaaagtttattttcttgatgcataacagtcttattcgtcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG
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--------------------------------------------------ttttatattttaatgattgtgaatatagcattttatttttatttttttattt------------attttgaataatttaataactt----ccaaaca-tttggtttgattgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAATATTTCAGCCTCATCTGTAGTCAGCAAATGGCGAG
upper sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G26100.1 (Glycine max), 3'ss of exon 6
gtgcgatgattctatctcgaatgtgtttttacttttgaactcttactctcttttgcatttcaattcatatgcacaccaaaccattaactaatttcttgagcctagctcaattagatcttgtaaagtttattttcttgatgcataacagtcttattcgtcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG
||| |||| ||| | || | | | | |||||| | | | | ||| | ||| | | || | | ||| | ||||| | | || | | || |||| |||||||||||||| ||||| ||||||||||| || || || || || || |||||||||||||| || ||||||||| |||
-------------------------------------------------ttttcatattttaatgattgtgaatat----------agcagtttctttttcttt-tttattta--ttttgaataattaaataactt----cctaaca-tttggtttgattgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAAGACTACTTTTTTTAATATTTCAGCCTCATCTGTAGTCAGCAAATGGCGAG
upper sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 6
gtgcgatgattctatctcgaatgtgtttttacttttgaactcttactctcttttgcatttcaattcatatgcacaccaaaccattaactaatttcttgagcctagctcaattagatcttgtaaagtttattttcttgatgcataacagtcttattcgtcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG
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--------------------------------------------------------------ttgcctttccaaatttctctgtcatgatgttgcttgatcatgctcttcttctaggttgaattgttaattgt--taat---tgaaatctccattcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAGMapped 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|124771328|gb|EH861458.1|EH861458EST: TAACTCCATGGAAAGGAATTCTTCTTTTTGGTCCTCCTGGTACCGGAAAG ACTATGCTTGCAAAGGCTGTTGCTACAGAGTG
genomic: TAACTCCATGGAAAGGAATTCTTCTTTTTGGTCCTCCTGGTACCGGAAAGgtgcgatgat ... tcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTG
EST:
gi|163982083|gb|ES156753.1|ES156753EST: AACTCCATGGAAAGGAATTCTTCTTTTTGGTCCTCCTTGGTACCGGAAAG ACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAAC
genomic: AACTCCATGGAAAGGAATTCTTCTTTTTGGTCCTCC-TGGTACCGGAAAGgtgcgatgat ... tcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAAC
EST:
gi|163991033|gb|ES146261.1|ES146261EST: TAACTCCATGGAAAGGAATTCTTCTTTTTGGTCCTCCTGGTACCGGAAAG ACTATGCTTGCAAAGGC
genomic: TAACTCCATGGAAAGGAATTCTTCTTTTTGGTCCTCCTGGTACCGGAAAGgtgcgatgat ... tcttgtgcagACTATGCTTGCAAAGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatcttgtaaagtttattttcttgatgcataacagtcttattcgtcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG
gcataac putative branch site (score: 3)
ttcgtctt putative PPT
ttgtaaagtttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgatgattctatctcgaatgtgtttttacttttgaactcttactctcttttgcatttcaattcatatgcacaccaaaccattaactaatttcttgagcctagctcaattagatcttgtaaagtttattttcttgatgcataacagtcttattcgtcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA