Sequence
atgc intronic sequence ATGC exonic sequencegtactccagtcgttacctataatgctgaatgtgtggaaagatacaattaaaaagtgaacacatccattgaagttgaatctgtggttcatttgaatgttgtaatgatcctatatgttcatgtttgcagCAAAACTGGAAGAACAACTCTAAATCTGGAAACCCGATGTTCATGGATCCAAGCAACCCGACATGGGGTTGGAGCTGGTTAGAGAGATGGATGGCTGGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03040.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03040.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G36270.1 (Glycine max), 3'ss of exon 5
gtactccagtcgttacctataatgctgaatgtgtggaaagatacaattaaaaagtgaacacatccattgaagttgaatctgtggttcatttgaatgttgtaatgatcctatatgttcatgtttgcagCAAAACTGGAAGAACAACTCTAAATCTGGAAACCCGATGTTCATGGATCCAAGCAACCCGACATGGGGTTGGAGCTGGTTAGAGAGATGGATGGCTGGTA
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-------------------gcattctgcctatgatatgattttcaatcataa---gtgtaagttccttgatgctg--tcaacaaattcagtgtttgatatttgggggcaaaaaatatttg---gcagCAAAACTGGAAGAACTCGTCTAGATCTGTAAATCCAATGTTTATGGATCCAACTAATCCGAGCTGGGGTTGGAGCTGGTTGGAACGATGGATGGCAGCCC
upper sequence: AT5G03040.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G33560.1 (Glycine max), 3'ss of exon 5
gtactccagtcgttacctataatgctgaatgtgtggaaagatacaattaaaaagtgaaca-catccattgaagttgaatctgtggttcatttgaatgttgtaatgatcctatatgttcatgtttgcagCAAAACTGGAAGAACAACTCTAAATCTGGAAACCCGATGTTCATGGATCCAAGCAACCCGACATGGGGTTGGAGCTGGTTAGAGAGATGGATGGCTGGTA
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-----------------catatt-ttgaatgaatagcattctgc--ctatgatataattttcaaccataagtgtaagttccttgatgc-tttgaacaaaatcagtgtttgacat-------ttggcagCAAAATTGGAAGAACTCATCTAGATCTGTAAATCCAATGTTCATGGATCCAACCAATCCAAGCTGGGGTTGGAGCTGGTTGGAACGATGGATGGCAGCCC
upper sequence: AT5G03040.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G20070.1 (Glycine max), 3'ss of exon 4
gtactccagtcgttacctataatgctgaatgtgtggaaagatacaattaaaaagtgaacacatccattgaagttgaatctgtggttcatttgaatgttgtaatgatcctatatgttcatgtttgcagCAAAACTGGAAGAACAACTCTAAATCTGGAAACCCGATGTTCATGGATCCAAGCAACCCGACATGGGGTTGGAGCTGGTTAGAGAGATGGATGGCTGGTA
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------------------agaata-tggatactagtttgagttccttgatattttgaacaaatt-attaaacttcaaagtttggtt---ttaaata----aataaatataaatgtatatcttgacagCAAAACTGGAAGAATGCATCAAGATCTGTAAACCCAATGTTCATGGATCCAACCAATCCAGCCTGGGGTTGGAGTTGGTTGGAACGATGGATGGCAGCCC
upper sequence: AT5G03040.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0040g02360.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------gtactccagtcgttacctataatgctgaatgtgtggaa---agatacaattaaaaagtga--acacatccattgaagttgaatctgtggttcatttgaatgttgtaatgatcctatatgttcatgtt--tgcagCAAAACTGGAAGAACAACTCTAAATCTGGAAACCCGATGTTCATGGATCCAAGCAACCCGACATGGGGTTGGAGCTGGTTAGAGAGATGGATGGCTGGTA
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gtatcctattcatcaatactgtttcctgcccattatccatttttaggatcaagaactcactggttggatcttccagttatcttggtatgaaatggaaagaaaatcaaataccagtggtgcactcat-gtagacacatgttttattattgcaaattcttgattaatccctgatggaattggtcctacagCAAGCGTGGAAGAATTCTTCAAAGTCCACAAACCTATTGTTCATGGATCCAAGCAACCCCCATTGGGGTTGGAGCTGGTTGGAACGATGGATGGCGGCCCMapped 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|47828004|gb|CK117688.1|CK117688EST: AGGCAACAATGAGAAGGGAAAGGGCATTGGCTTATTCATACTCTCATCAG CAAAACTGGAAGAACAACTCTAAATCTGGAAACCCGATGTTCATGGATCCA
genomic: AGGCAACAATGAGAAGGGAAAGGGCATTGGCTTATTCATACTCTCATCAGgtactccagt ... atgtttgcagCAAAACTGGAAGAACAACTCTAAATCTGGAAACCCGATGTTCATGGATCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaatctgtggttcatttgaatgttgtaatgatcctatatgttcatgtttgcagCAAAACTGGAAGAACAACTCTAAATCTGGAAACCCGATGTTCATGGATCCAAGCAACCCGACATGGGGTTGGAGCTGGTTAGAGAGATGGATGGCTGGTA
atttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactccagtcgttacctataatgctgaatgtgtggaaagatacaattaaaaagtgaacacatccattgaagttgaatctgtggttcatttgaatgttgtaatgatcctatatgttcatgtttgcagCAAAACTGGAAGAACAACTCTAAATCTGGAAACCCGATGTTCATGGATCCAAGCAACCCGACATGGGGTTGGAGCTGGTTAGAGAGATGGATGGCTGGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA