Sequence
atgc intronic sequence ATGC exonic sequencegtagcttctctttcacatatcatctcttataagatccaacaagggcatcattttgctaacaattatcccttaattttgattgtgtagCCGGAGAATCTGTTGTTAACTTTAGATGGGCACATAAAGATTGCTGATTTTGGTAGCGTAAAGCCAATGCAAGACAGCCAAATCACAGTGCTTCCTAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G10540.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g65230.1 (Oryza sativa), 3'ss of exon 4
gtagcttctctttcacatatcatctcttataagatccaacaagggcatcattttgctaacaattatccc--ttaattttgattgtgtagCCGGAGAATCTGTTGTTAACTTTAGATGGGCACATAAAGATTGCTGATTTTGGTAGCGTAAAGCCAATGCAAGACAGCCAAATCACAGTGCTTCCTAATG
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---gttcgcaaatcgtat-tggggttgcacattggcctgcagcagtaat-tatgggtggctgtaactcacactgctcttgatctttcagCCAGAAAATTTACTGCTTACTTCTGATGGGCACATCAAGATTGCCGATTTTGGTAGTGTGAAGCCTACAAAGGACACCCCGATCAAAGTCCTTCCAAATT
upper sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G097821_T02 (Zea mays), 3'ss of exon 4
------gt-agcttctctttcacatatcatctcttataagatccaacaagggcatcat-tttgctaacaattatcccttaattttgattgtgtagCCGGAGAATCTGTTGTTAACTTTAGATGGGCACATAAAGATTGCTGATTTTGGTAGCGTAAAGCCAATGCAAGACAGCCAAATCACAGTGCTTCCTAATG
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gtgagtgtgaaatgaaaatcaagatggagttgcccatgacacagtatgtttatgtcatatttgctatttgacaaggactg-cattggtctttcagCCAGAAAATCTACTGCTTACTTCTGATGGGCACATCAAGATTGCTGACTTTGGTAGTGTGAAGCCTACAAGGGATACTCCTATCAAAGTTCTCCCAAATTMapped 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|86070404|gb|DR366161.1|DR366161EST: ATGCTCTTGAGTATATACATAATATGGGACTGATACATCGAGATATTAAG NNNGAGAATCTGTTGTTAACTTTAGATGGGCACATAAAGATTGCTGATTTT
genomic: ATGCTCTTGAGTATATACATAATATGGGACTGATACATCGAGATATTAAGgtagcttctc ... gattgtgtagCCGGAGAATCTGTTGTTAACTTTAGATGGGCACATAAAGATTGCTGATTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatccaacaagggcatcattttgctaacaattatcccttaattttgattgtgtagCCGGAGAATCTGTTGTTAACTTTAGATGGGCACATAAAGATTGCTGATTTTGGTAGCGTAAAGCCAATGCAAGACAGCCAAATCACAGTGCTTCCTAATG
ttaattttgattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcttctctttcacatatcatctcttataagatccaacaagggcatcattttgctaacaattatcccttaattttgattgtgtagCCGGAGAATCTGTTGTTAACTTTAGATGGGCACATAAAGATTGCTGATTTTGGTAGCGTAAAGCCAATGCAAGACAGCCAAATCACAGTGCTTCCTAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA