Sequence
atgc intronic sequence ATGC exonic sequencegtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttactactgatagaaatcgtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.2 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 16
gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttactactgatagaaatcgtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
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------------------------------------------------------------------------catttctacgtactagtaatagttgccaccagttttttagtctatatatgt-atatgctaatccagagttttgaattaactttat------ctttgtatatatttagACCAGATCGAGAAAGCGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCGTCAAGTTAAAGCAGTTCTTGAGGAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 12
gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttactactgatagaaatcgtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
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-------------------------------------------------------------------------gccatttctacgtactagtaatagttgccaccagttttttagtctatatgtgtatgctaagccagagttttgaattaactttat------ctttgtatatatttagACCAGATCGAGAAAGTGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCATCAAGTTAAAGCAGTTCTTGAGGAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 12
gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttactactgatagaaatcgtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
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----------------------------------------------------------------------ttgccattcctgttggcaagtaattttatgggtttt------ctgatcagtatatttttattatttcaagggttttgaaataactatag-ctgtatatattatgt--agACCAGATCGAGAAAGTGATAGTGAGGCTGAAG---TCGAGCACGCTGAAAAGCTCCGTCAAGTTAAAGCTGTCCTTGAAGAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 14
gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttac-tactgatagaaatcgtgtttacagttgaaatc--tagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
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-----------------------------------------------------------------------------taactgaaaatggcaaacacacttttaatttgcatattgac-----tcttatgctaggatagcattaatgattatgaactaatgacaaaatttcatattatttagACCTGGTCGAGAAAGTGACAGTGAAGCAGAAGATCTTGAGCATGCTGAAAAACTTCGTCAAGTTAAAGCAGTCCTTGAAGAGMapped 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|19874907|gb|AU235738.1|AU235738EST: CAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG ACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAA
genomic: CAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAGgtaccaaaaa ... ttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
tggtcttcctttttta CT-rich tract
ttttttatcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttactactgatagaaatcgtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA