Sequence
atgc intronic sequence ATGC exonic sequencegtcttcgtgagattattgttatatctggattccgattcttgaagaaaaccgtgcattgttgctgattacatgactttattcatctattagGGAGAGCTTCAATACTTCATCGGTGTGCAGCTTGATGGAAGTGATCATGTAGAGCCCCTCCAAAATCGTTTGTCTGAGAGAACAGAGATGCAGAGTTCGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G58140.4 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os04g23890.4 (Oryza sativa), 3'ss of exon 8
-----------gtcttcgtgagat--tattgttata---tctgga--ttccgattcttgaagaaaaccgtgcattgttgctgattacatgactttattcatctat-----tagGGAGAGCTTCAATACTTCATCGGTGTGCAGCTTGATGGAAGTGATCATGTAGAGCCCCTCCAAAATCGTTTGTCTGAGAGAACAGAGATGCAGAGTTCGA
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gtatctgaaaaatctgtgccaaatgctactcccaagtattttggagcttgcaatttttaactagtagtgggtatgattactacatggtagtgattgcacatctgtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCA
upper sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 10
-------------------------------gtcttcgtgagattattgttatatctggattccgattcttgaagaaaaccgtgcattgttgctgattacatgacttt-attcatctat---tagGGAGAGCTTCAATACTTCATCGGTGTGCAGCTTGATGGAAGTGATCATGTAGAGCCCCTCCAAAATCGTTTGTCTGAGAGAACAGAGATGCAGAGTTCGA
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gtgaaagtgatactgttatgctagaaaacaaataatttgaacataaacattcaatatctattaaactatatattgtcttcccccctttctagtttctaatgttattctcaatgatttgtatttagGGTGAACTTCAATACTTCATTGGTGTTCAACTAGATGGAAGTGATCATGTAGAACCCTTAAAAAACCGCCTGTCTGAGACAACTGAGCAACAAAGTGCTA
upper sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G33560.1 (Glycine max), 3'ss of exon 8
--------------gtcttcgtgagattattgttatatctggattccgattcttgaaga------aaaccgtgcattgt----------tgctgattac--atgactttat---tcatctat---tagGGAGAGCTTCAATACTTCATCGGTGTGCAGCTTGATGGAAGTGATCATGTAGAGCCCCTCCAAAATCGTTTGTCTGAGAGAACAGAGATGCAGAGTTCGA
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gtgaatgtgatactgttatggt-agaaaacaatta-atctgaatcatgaacattcaatatctattaaacaatacattgtgttcccccctttttagtttctaatgtttttctcaatgatttgtatttagGGTGAACTTCAATACTTCATTGGTGTTCAACTAGATGGAAGTGATCATGTAGAACCCTTAAAAAACCGCCTGTCTGAGACAACTGAGCAACAAAGTGCTAMapped 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|125014201|gb|EL086470.1|EL086470EST: GAAAGAAATTCTGGAACTTATTCCACTTGCAACCTATGCGTGATCAGAAG GGAGAGCTTCAATACTTCATCGGTGTGCA
genomic: GAAAGAAATTCTGGAACTTATTCCACTTGCAACCTATGCGTGATCAGAAGgtcttcgtga ... catctattagGGAGAGCTTCAATACTTCATCGGTGTGCA
EST:
gi|124723412|gb|EH814814.1|EH814814EST: CGTGATCAGAAG GGAGAGCTTCAATACTTCATCGGTGTGCAGCTTGATGGAAGTGATCATGTA
genomic: CGTGATCAGAAGgtcttcgtga ... catctattagGGAGAGCTTCAATACTTCATCGGTGTGCAGCTTGATGGAAGTGATCATGTA
EST:
gi|164224528|gb|ES078251.1|ES078251EST: GAAAGAAATTCTGGAACTTATTCCACTTGCAACCTATGCGTGATCAGAAG GGAGAGCT-CAATACTTCATCGGTGTGCAGCTTGATGGAAG
genomic: GAAAGAAATTCTGGAACTTATTCCACTTGCAACCTATGCGTGATCAGAAGgtcttcgtga ... catctattagGGAGAGCTTCAATACTTCATCGGTGTGCAGCTTGATGGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgaagaaaaccgtgcattgttgctgattacatgactttattcatctattagGGAGAGCTTCAATACTTCATCGGTGTGCAGCTTGATGGAAGTGATCATGTAGAGCCCCTCCAAAATCGTTTGTCTGAGAGAACAGAGATGCAGAGTTCGA
tgctgat putative branch site (score: 3)
ctttattc putative PPT
tttattcatctatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcttcgtgagattattgttatatctggattccgattcttgaagaaaaccgtgcattgttgctgattacatgactttattcatctattagGGAGAGCTTCAATACTTCATCGGTGTGCAGCTTGATGGAAGTGATCATGTAGAGCCCCTCCAAAATCGTTTGTCTGAGAGAACAGAGATGCAGAGTTCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG