Sequence
atgc intronic sequence ATGC exonic sequencegtaaagaggtggttacaaaatcttgttgaccttaggatcttgaagttgggagacttacaatagactctgattagttttcaagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03030.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03030.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os12g40880.2 (Oryza sativa), 3'ss of exon 7
gtaaagaggtggttacaaaatcttgttgaccttaggatcttgaagttgggagacttacaatagactctgattagttttcaagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCA--------------------------
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--gtgttaccagtttcactgtcaagtattctattaca-cataacattgtg---ttttgactgatcgctgaaacatctttg---tctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCAGTGAGTTATCATTGCAGATCCAGAAT
upper sequence: AT1G03030.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os12g40880.1 (Oryza sativa), 3'ss of exon 7
gtaaagaggtggttacaaaatcttgttgaccttaggatcttgaagttgggagacttacaatagactctgattagttttcaagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCA
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--gtgttaccagtttcactgtcaagtattctattaca-cataacattgtg---ttttgactgatcgctgaaacatctttg---tctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCA
upper sequence: AT1G03030.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G035338_T01 (Zea mays), 3'ss of exon 7
gtaaagaggtggttacaaaatcttgttgaccttaggatcttgaa-gttgggagacttacaatagactctgattagttttcaagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCA
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--------gtatctaccagtgccctgcaatac-aaattcttgaatactgcatgctatttaatctgatcctctaaacatcttgg-tttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA
upper sequence: AT1G03030.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G34390.1 (Glycine max), 3'ss of exon 7
-gtaaagaggtggttacaaaatcttgttgaccttaggatcttgaagttgggagacttac--aatagactctgattagtttt-------caagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCA
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agctgggatgcacagaaagaacagtaagcatctgtgcactgacatgatggagttcttatctgctttgttctgttgcattttggtgaaacaaattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA
upper sequence: AT1G03030.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G31550.1 (Glycine max), 3'ss of exon 6
---------gtaaagaggtggttacaaa-atct---tgttgaccttaggatcttgaagttgggagacttacaatagactctgattagttttcaagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGA-AGATGATATCTTTGTTAGCCTCCA-------------------------
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agctggggtgcacagaaagagcagtaagcatccgtgcattgacatgacggaattcttatctgctttgttctgttgcattttggtgaaatttt---tttttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTAAGATGTGGTCCACTCATCAGCATTTTATAAATTTCTGACACAAATTATGAT
upper sequence: AT1G03030.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0141g00310.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------------------------------------gtaaagaggtggttacaaaatcttgttgaccttaggatcttgaag--ttgggagac-------------ttacaatagactctgattagttttcaagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCA
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gtgagtagctattgatgttggctgcgtcattttattcttgttgagactttagaactggttggtgcataaacttatctttttttttttttttcaaaaataaaaaataaaaaatttgtggtacatgagtacttttctcatattgcattatgatgagcaat-attttctgtagGGGTCAGTTTATGCACCATCGTTTGATCATGGTGTTGGAGATCCAGTTGAAGATGATATATTTATCAGCCTCCAMapped 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|86085201|gb|DR380960.1|DR380960EST: CTTTTGATCCTGCACTACTGCTTAACTGTTTAAAGAAGCTGAAAAACGAG GGCTCAGTTTATGTGCCATCATTCGATCATGGAGTTGGGGATCCAGTTGAA
genomic: CTTTTGATCCTGCACTACTGCTTAACTGTTTAAAGAAGCTGAAAAACGAGgtaaagaggt ... agctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcttgaagttgggagacttacaatagactctgattagttttcaagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCA
ctttcc CT-rich tract
attagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagaggtggttacaaaatcttgttgaccttaggatcttgaagttgggagacttacaatagactctgattagttttcaagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG