Sequence
atgc intronic sequence ATGC exonic sequencegtaaatgcctagtctgtctgattctgaacattgatggattgttttaaaaaagaattagaggatgataaaatattcttgtggtcttcagGGCTTGATGCCTTCCAGGCTGAGAAAGTGATGGAGACATTGCAAAAGCTTGCACAGGATGGACATACTGTGATCTGCTCCATACACCAGCCTAGAGGTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G01320.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G01320.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G119345_T01 (Zea mays), 3'ss of exon 4
---------gtaaatgccta-gtctgtctgat--tctgaacattgatggattgttttaaaaaagaattagaggatgata-aaatat-tcttgtggtcttcagGGCTTGATGCCTTCCAGGCTGAGAAAGTGATGGAGACATTGCAAAAGCTTGCACAGGATGGACATACTGTGATCTGCTCCATACACCAGCCTAGAGGTTC
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tcataaacagtagtcatcaacatctgtttggtcatctgacaat--atgaaaatgtcaaatattaagttatatttttttgtatgtatgtgatttgtcttttagGCCTTGATGCCTTCCAAGCTGAGAAGGTCATGGAGACTCTTCGTCAACTTGCTCAGGATGGGCACACTGTTATCTGTTCGATACACCAGCCAAGAGGTTC
upper sequence: AT2G01320.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G26160.1 (Glycine max), 3'ss of exon 4
---------gtaaatgcct---agtctgtctgattc---tgaacattgatggattgttttaaaaaagaattagaggatgataaaatattcttgtg-gtcttcagGGCTTGATGCCTTCCAGGCTGAGAAAGTGATGGAGACATTGCAAAAGCTTGCACAGGATGGACATACTGTGATCTGCTCCATACACCAGCCTAGAGGTTC
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tcccagccagtagctgcttccaaatgcagtcaatttgtacagacaatcataacctctctctccacatattttg----tcatgaagttgttttctgtgttttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCGATACATCAGCCAAGAGGTTC
upper sequence: AT2G01320.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G41110.1 (Glycine max), 3'ss of exon 4
gtaaatgcctagtctgt--ctgattctgaacattgatggattgttttaaaaa--agaa-----------ttagaggatgataaaatattcttgtg-gtcttcagGGCTTGATGCCTTCCAGGCTGAGAAAGTGATGGAGACATTGCAAAAGCTTGCACAGGATGGACATACTGTGATCTGCTCCATACACCAGCCTAGAGGTTC
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----tttcccagccagtcgctgcttccaaatgcggtcaatttgcacagacaatcataacctctctccacttattttgtcatgaagttgttttctgtgctttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCTATACATCAGCCAAGAGGGTC
upper sequence: AT2G01320.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0011g04670.t01 (Vitis vinifera), 3'ss of exon 4
----------gtaaatgcctagtc-tgtctgattctgaacattgatggattgttttaaaaaagaattagaggatgataaaata-ttcttgtggtcttcagGGCTTGATGCCTTCCAGGCTGAGAAAGTGATGGAGACATTGCAAAAGCTTGCACAGGATGGACATACTGTGATCTGCTCCATACACCAGCCTAGAGGTTC
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ttctttttttctccataactattggcatgagagttttgctagtagtgaagcccacataagcttctatggtttgtaaccaaataactgatggtgcttgtagGACTCGATGCTTTCCAGGCAGAAAAGGTGATGGAGACACTCCGACTACTTGCACAGGATGGACACACTGTAATTTGTTCCATACACCAGCCTAGAAGTTCMapped 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|164178327|gb|ES066750.1|ES066750EST: GTCCCTCTGTCATATTTGCTGATGAACCTACCACTG GGCTTGATGCCTTCCAGGCTGAGAAAGTGATGGAGACATTGCAAAAGCTTG
genomic: GTCCCTCTGTCATATTTGCTGATGAACCTACCACTGgtaaatgcct ... tggtcttcagGGCTTGATGCCTTCCAGGCTGAGAAAGTGATGGAGACATTGCAAAAGCTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggattgttttaaaaaagaattagaggatgataaaatattcttgtggtcttcagGGCTTGATGCCTTCCAGGCTGAGAAAGTGATGGAGACATTGCAAAAGCTTGCACAGGATGGACATACTGTGATCTGCTCCATACACCAGCCTAGAGGTTC
cattgat putative branch site (score: 4)
ttcttgt putative PPT
ttgttttaaaaaagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatgcctagtctgtctgattctgaacattgatggattgttttaaaaaagaattagaggatgataaaatattcttgtggtcttcagGGCTTGATGCCTTCCAGGCTGAGAAAGTGATGGAGACATTGCAAAAGCTTGCACAGGATGGACATACTGTGATCTGCTCCATACACCAGCCTAGAGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA