Sequence
atgc intronic sequence ATGC exonic sequence...tgttcttgtaccaacattcttttgtacgaaacttttcacttgggaaaatttgatccatcttgtaggttgtttaactgatattttcaactcctttttacagGGTTTTGCTTCAGGTCTGATGTTGAGCATATCGTTCTTGGATTTGGCTCATAATGCTATAAACTCTATTGGGTTCTTTAAAGCCAACCTCTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G20870.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G41580.5 (Glycine max), 3'ss of exon 2
-----------------------------------------------tgttcttgtaccaacattcttttgt-acgaaacttttcacttgggaaaatttgatccatcttgtaggttgt-ttaactgatattttcaactcctttttacagGGTTTTGCTTCAGGTCTGATGTTGAGCATATCGTTCTTGGATTTGGCTCATAATGCTATAAACTCTATTGGGTTCTTTAAAGCCAACCTCTGG
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gtagttttagtttatgagaatgcattgattcagttagaatcattctgtccctttctctctttagtcaaatgtgatgaaatgtattctatttgttggtttgctttgcttggtcaattctgttttctgaaactatt--tcattgtatgaagGGTTTTGCTGCTGGTTTGATGCTTAGCATATCGTTCTTTGATTTGGCTCACAATGCTTTGAACTCATTGGGCTTCTTGAAAGGCAACCTTTGG
upper sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G03820.2 (Glycine max), 3'ss of exon 2
--------------------------------------------------------tgttcttgta-ccaacattcttttgtacgaaacttt--tcacttggga--aaatttgatccatcttgtaggttgttta------actgatattttcaactccttt-ttaca----gGGTTTTGCTTCAGGTCTGATGTTGAGCATATCGTTCTTGGATTTGGCTCATAATGCTATAAACTCTATTGGGTTCTTTAAAGCCAACCTCTGG
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gtagttttagttggtcaggaattttatttatttatttattttaatttatgagaatgcattgattcagttagaatcattctgtccctctctttagtcaaatgtgatgaaatgtattctatttgttggtttgcttgctcaattctgttttcttaaactgtttcattgcatgaagGGTTTTGCTGCTGGTTTGATGCTTAGCATATCGTTCTTTGATTTGGCCCACAATGCTTTGAACTCACTGGGCTTCTTGAAAGGAAACCTTTGG
upper sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G06060.1 (Glycine max), 3'ss of exon 1
tgttcttgtaccaacattcttttgtacgaaacttttcacttgggaaaatttgatc-catcttgtaggt---tgtttaactgatattttcaactcctttttacagGGTTTTGCTTCAGGTCTGATGTTGAGCATATCGTTCTTGGATTTGGCTCATAATGCTATAAACTCTATTGGGTTCTTTAAAGCCAACCTCTGG
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---tttgtcatttataaaatgtaacattaag-tctacaattaaaatccttgacttgcatactttagccatatgcttgctttttgaaagctatcatttcatgaagGGTTTTGCTGCTGGTTTGATGTTGAGTATATCATTCTTTGATCTGACTCATAATGCCTTGAACTCACTTGGCTTCTTGAGAGGCAACCTTTGG
upper sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 2
tgttcttgtaccaacattcttttgtacga---aacttttcact--tgggaaaattt--gatccatcttgtaggttgtttaactgatattttcaactcctttttacagGGTTTTGCTTCAGGTCTGATGTTGAGCATATCGTTCTTGGATTTGGCTCATAATGCTATAAACTCTATTGGGTTCTTTAAAGCCAACCTCTGG
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-------aagccagggttctggagcatcatctaagtttaagctgtcagaggcattccagatttattatgcagtaaaattgtttggatatctggatttcttcatgtagGGATTTGCTGCAGGCCTCATGCTGAGCATATCTTTCCTAGATTTGGCTCATAATGCTTTGAACTCCATCGGCTTCTTAAAAGGAAACCTTTGGMapped 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|116403230|gb|EG445822.1|EG445822EST: TTGTAGTTCTTAGTGAGACTCCCAATATGAAGATGCTTGGACTTCTACAG GGTTTTGCTTCAGGTCTGATGTTGAGCATATCGTTCTTGGATTTGGCTCAT
genomic: TTGTAGTTCTTAGTGAGACTCCCAATATGAAGATGCTTGGACTTCTACAGgtgacgatgc ... ctttttacagGGTTTTGCTTCAGGTCTGATGTTGAGCATATCGTTCTTGGATTTGGCTCAT
EST:
gi|124983156|gb|EL055908.1|EL055908EST: AAGATGCTTGGACTTCTACAG GGTTTTGCTTCAGGTCTGATGTTGAGCATATCGTTCTTGGATTTGGCTCAT
genomic: AAGATGCTTGGACTTCTACAGgtgacgatgc ... ctttttacagGGTTTTGCTTCAGGTCTGATGTTGAGCATATCGTTCTTGGATTTGGCTCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatttgatccatcttgtaggttgtttaactgatattttcaactcctttttacagGGTTTTGCTTCAGGTCTGATGTTGAGCATATCGTTCTTGGATTTGGCTCATAATGCTATAAACTCTATTGGGTTCTTTAAAGCCAACCTCTGG
aactgat putative branch site (score: 3)
ttttcaactccttttt CT-rich tract
tttaactgatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttcttgtaccaacattcttttgtacgaaacttttcacttgggaaaatttgatccatcttgtaggttgtttaactgatattttcaactcctttttacagGGTTTTGCTTCAGGTCTGATGTTGAGCATATCGTTCTTGGATTTGGCTCATAATGCTATAAACTCTATTGGGTTCTTTAAAGCCAACCTCTGG
- - - - taccaac
- - - - - - - - - - - - -acgaaac