Sequence
atgc intronic sequence ATGC exonic sequencegtttcgtcttgatcatatttatatcattttagttttttataattgccaggggatatcatcactgagaactttaatatatgcagCTATTTTCACTTTGTTCATGAGTTTGTAACTATACTTATGGACTCTGCAATTTTGTTCTTTGGGATCTTGCCTTGGTTTTGGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01320.1 |
intron # | 2 |
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 2
lower sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------gtttcgtcttg-atcatatttatatcattttagttttttataattg---ccaggggatatcatcactgagaactttaatat-atgcagCTATTTTCACTTTGTTCATGAGTTTGTAACTATACTTATGGACTCTGCAATTTTGTTCTTTGGGATCTTGCCTTGGTTTTGGAAG
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gtttgttcctgaatatatgtgaatttctttcattggatgatgctatcttattctcaaggttgcttctggtatatttttttcataattgtgtatttctgttattgtatcttgttagcatttttacaaattccttttttgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 2
---------------------gtttcgtcttgatcatatttat-atcattttagttttttataattgccaggggata---tcatcactgagaactttaatatatg-----------------cagCTATTTTCACTTTGTTCATGAGTTTGTAACTATACTTATGGACTCTGCAATTTTGTTCTTTGGGATCTTGCCTTGGTTTTGGAAG
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gtttgtcttcttatttctattgatttctcttgaa-gtatggatgattacaccagactatcagacttcttcatgcatagtttatttgttctgacctctactgtctgtcctatctctcttttttcagCCACTTCCATTTTGTTCATGAGTGCGTTACTATATTAATGGACTCTGCAATTTTGTTCTTTGGAGTATTGCCTTGGTTTTGGAAGMapped 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|86066466|gb|DR362223.1|DR362223EST: ATTAGCCAAGAGAAGTTTGAGAAATCACGAGCATACAGTCTTGACAAAAG CTATTTTCACTTTGTTCATGAGTTTGTAACTATACTTATGGACTCTGCAAT
genomic: ATTAGCCAAGAGAAGTTTGAGAAATCACGAGCATACAGTCTTGACAAAAGgtttcgtctt ... atatatgcagCTATTTTCACTTTGTTCATGAGTTTGTAACTATACTTATGGACTCTGCAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagttttttataattgccaggggatatcatcactgagaactttaatatatgcagCTATTTTCACTTTGTTCATGAGTTTGTAACTATACTTATGGACTCTGCAATTTTGTTCTTTGGGATCTTGCCTTGGTTTTGGAAG
ctttaat putative branch site (score: 4)
agaactttaatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttcgtcttgatcatatttatatcattttagttttttataattgccaggggatatcatcactgagaactttaatatatgcagCTATTTTCACTTTGTTCATGAGTTTGTAACTATACTTATGGACTCTGCAATTTTGTTCTTTGGGATCTTGCCTTGGTTTTGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG