Sequence
atgc intronic sequence ATGC exonic sequencegtaacaatttgaaattttttaggaaaagtttttttttatgtggttcagttgagaatttggttggacaatgttttagGTACTTTGCACCTGAATATTTCATGCACGGAATCGTGGACGAGAAGACTGATGTTTTCGCTTTTGGAGTTCTCCTCTTGGAGCTCATAACCGGACATCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05140.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G29860.1 (Glycine max), 3'ss of exon 4
gta-acaatttgaaatttttta--ggaaaagtttttt---tttatgtggttcagt-tgagaatttggttggacaatgttttagGTACTTTGCACCTGAATATTTCATGCACGGAATCGTGGACGAGAAGACTGATGTTTTCGCTTTTGGAGTTCTCCTCTTGGAGCTCATAACCGGACATCCT
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gtatgcaaataaaaaattactaacgctagagttcagtaggttctcgtgatttaatatattcacctaattacttgat-tggcagCTACTTTGCTCCTGAATATTTCATGCATGGAATAGTAGATGAGAAAACTGATGTTTTTTCATTTGGGGTCCTACTTTTGGAGATCATAACTGGGCGTCCA
upper sequence: AT3G05140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G37470.1 (Glycine max), 3'ss of exon 4
--gtaacaatttgaaattttttagga---aaagtttttt---tttatgtggttcagttgagaa-tttggttggacaatgttttagGTACTTTGCACCTGAATATTTCATGCACGGAATCGTGGACGAGAAGACTGATGTTTTCGCTTTTGGAGTTCTCCTCTTGGAGCTCATAACCGGACATCCT
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gtataaaaataaaaaatttactaatgcttggagttttataaattttcatgatttaataaattcctctaattacttgat-tggcagCTATTTTGCTCCTGAATATTTCATGCATGGAATAGTAGATGAGAAAACTGATGTTTTTTCATTTGGGGTCCTACTTTTGGAGATCATAACTGGGCGTCCA
upper sequence: AT3G05140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ26733 (Selaginella moellendorffii), 3'ss of exon 4
gtaacaatttgaaattttttaggaaaagtttttttttatgtggttcagttgagaatttggttggacaatgtt---ttagGTACTTTGCACCTGAATATTTCATGCACGGAATCGTGGACGAGAAGACTGATGTTTTCGCTTTTGGAGTTCTCCTCTTGGAGCTCATAACCGGACATCCT
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-----------------------gtgagccatccactcttcaaactgtttgtga-cttgacaagtctgtcctgaaccagGTACCTCGCACCGGAATACTTCATGCACGGCATTGTGGACGAGAAAACCGATGTATTCGCATATGGAGTGCTGCTTCTCGAGCTCATCACCGGACGGAAG
upper sequence: AT3G05140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ26422 (Selaginella moellendorffii), 3'ss of exon 4
gtaacaatttgaaattttttaggaaaagtttttttttatgtggttcag--ttgagaatttggttggacaatgttttagGTACTTTGCACCTGAATATTTCATGCACGGAATCGTGGACGAGAAGACTGATGTTTTCGCTTTTGGAGTTCTCCTCTTGGAGCTCATAACCGGACATCCT
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------------------gtgagccatccactcttcaaactgtttgtgacttgacaagtttgtcc-----tgaaccagGTACCTCGCACCGGAATACTTCATGCACGGCATTGTGGACGAGAAAACCGATATATTCGCATATGGAGTGCTGCTTCTCGAGCTCATCACCGGACGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaaaagtttttttttatgtggttcagttgagaatttggttggacaatgttttagGTACTTTGCACCTGAATATTTCATGCACGGAATCGTGGACGAGAAGACTGATGTTTTCGCTTTTGGAGTTCTCCTCTTGGAGCTCATAACCGGACATCCT
agtttttttttatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacaatttgaaattttttaggaaaagtttttttttatgtggttcagttgagaatttggttggacaatgttttagGTACTTTGCACCTGAATATTTCATGCACGGAATCGTGGACGAGAAGACTGATGTTTTCGCTTTTGGAGTTCTCCTCTTGGAGCTCATAACCGGACATCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA