Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcgtatttccaacactaccttgtgacttacgtttttttatcagagatgtggattaaatttgcttctaaattctgttgacagCAAACAATATGGATGTTCATTAGGGACATGATCAAAGGAACATTCCTCTCTGTCATACTAGGCCCACCCATTGTTGCTGCGATAATTTTCATAGTCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01320.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 5
------------------------------------------------------------------------gtatgtcgtatttccaacac----taccttgtgactt----acgtttttttatcagagatgtggatt--aaatttgcttctaaattctgttgacagCAAACAATATGGATGTTCATTAGGGACATGATCAAAGGAACATTCCTCTCTGTCATACTAGGCCCACCCATTGTTGCTGCGATAATTTTCATAGTCCAG
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gtatgtttgtgttctcaattttagcacctcagttattatatgttttaacatttgaatggtgttcacctgcaagattagtgaagtacaaaagtatcttggcttatgaatttgctatgttctaatccccaacatatttattctgaacctctagctttggacttttttcagCAAACTATTTGGCTCTTCATTAGGGACATGATCAAAGGGATTTTGCTATCCATCTTACTTGGACCTCCTATTGTGGCTGCTATTATCATCATAGTACAG
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------------------------gtatgtcgtatttccaacactacct-----tgtga----cttacgtttttttatcagaga--tgtggattaaatttgcttctaaattctgt-tgacagCAAACAATATGGATGTTCATTAGGGACATGATCAAAGGAACATTCCTCTCTGTCATACTAGGCCCACCCATTGTTGCTGCGATAATTTTCATAGTCCAG
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gtgtgttcatatttttttgtttttccttgtatttgttgctagctaggggtaggaatatacattgaaatttggcaacttgcagtgttttataactactgaagtaactgggcttatgaatttcttatcttcattttcctgatacttttatactgagatttctattgcttcatgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCCATGATATTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 5
------------gtatgtcgtatttccaacactaccttgtgacttacgtttttttatcagaga-tgtggattaaatttgctt-ctaaattctgttgacagCAAACAATATGGATGTTCATTAGGGACATGATCAAAGGAACATTCCTCTCTGTCATACTAGGCCCACCCATTGTTGCTGCGATAATTTTCATAGTCCAG
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gtcatggtttaaatttcttgtctttgaatttctttcgctttattccttatttattgttagagtctgttcctaatatttattttctctctattgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCCATTTTACTTGGGCCACCCATCGTGGCTGCAATCATTGTTATAGTACAGMapped 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|124753435|gb|EH843565.1|EH843565EST: TTCGTGATCGAGTCTCGGCATGGGTTCAACAAA CAAACAATATGGATGTTCATTAGGGACATGATCAAAGGAACATTCCTCTCT
genomic: TTCGTGATCGAGTCTCGGCATGGGTTCAACAAAgtatgtcgta ... ctgttgacagCAAACAATATGGATGTTCATTAGGGACATGATCAAAGGAACATTCCTCTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacgtttttttatcagagatgtggattaaatttgcttctaaattctgttgacagCAAACAATATGGATGTTCATTAGGGACATGATCAAAGGAACATTCCTCTCTGTCATACTAGGCCCACCCATTGTTGCTGCGATAATTTTCATAGTCCAG
ttctaaa putative branch site (score: 2)
ttctgtt CT-rich tract
tttttttatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcgtatttccaacactaccttgtgacttacgtttttttatcagagatgtggattaaatttgcttctaaattctgttgacagCAAACAATATGGATGTTCATTAGGGACATGATCAAAGGAACATTCCTCTCTGTCATACTAGGCCCACCCATTGTTGCTGCGATAATTTTCATAGTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC