Sequence
atgc intronic sequence ATGC exonic sequence...ctataagacaggctacatgaatgaacaatctatatatcttactctcttagtatctgcttagtttcttgaaaaactcatccactcgccttaatcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAACTTGATTGGATACTGTGCAGAGAAAGGCCAACACATGCTTATATATGTTTACATGAGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G54590.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G36140.1 (Glycine max), 3'ss of exon 3
ctataagacaggctacatgaatga-acaatctatatatct-tactctcttagtatctgcttagtttcttgaaaaactcatccactcgccttaatcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAACTTGATTGGATACTGTGCAGAGAAAGGCCAACACATGCTTATATATGTTTACATGAGTA
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ctgttgcgaagtattaaggtatcatgtagtcaatatttctgtatgatctttccgcttgtttgccaatctaaaccttttatgttcttttatt--ttttctcagGTTATGTTGTTGGGAAGGTTACATCATAGAAATCTGGTCAATTTGGTCGGGTATTGTGCAGAAAAAGGACAACACATGCTTGTATATGTCTACATGAGTA
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G41510.1 (Glycine max), 3'ss of exon 3
-ctataagacaggctacatgaatgaacaatctatatatcttactctcttagtatctgcttagtttcttgaaaaactcatccactcgccttaatcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAACTTGATTGGATACTGTGCAGAGAAAGGCCAACACATGCTTATATATGTTTACATGAGTA
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tttacagtccttatcatatacaatcactttctgtacttcctttctttttactccaagagtcattttcaattgtaacagttta-tgatctactttttttcagGTCATGTTGTTGGGAAGGTTACACCATAGAAATCTGGTGAATTTGGTTGGATATTGTGCAGAAAAGGGGAAACATATGCTTGTATATGTATACATGAGTA
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv19s0014g04960.t01 (Vitis vinifera), 3'ss of exon 2
ctataagacaggctacatg--aatgaacaatcta-tatatcttactctcttagtatctgcttagtttcttgaaaaactcatccactcgccttaatcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAACTTGATTGGATACTGTGCAGAGAAAGGCCAACACATGCTTATATATGTTTACATGAGTA
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-catgaatgttcctgcctcttactgcaaaatgtaataaacacttttccccttatggtagctttgcttgttattacattaccctatttttatt--tgttctcagGTTCACTTACTGGGAAGGTTACATCATAGAAACCTCGTGAATTTGGTTGGGTATTGTGCCGAAAAGGGCCAGCATATGCTTATATATGTCTACATGAGTAMapped 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|125088738|gb|EL147365.1|EL147365EST: AAGTTCTAGCCACTGATTCTAAACAGGGCGAAAAAGAGTTTCAGACAGAG GTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAA
genomic: AAGTTCTAGCCACTGATTCTAAACAGGGCGAAAAAGAGTTTCAGACAGAGgtaagatata ... atcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttagtatctgcttagtttcttgaaaaactcatccactcgccttaatcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAACTTGATTGGATACTGTGCAGAGAAAGGCCAACACATGCTTATATATGTTTACATGAGTA
ccttaat putative branch site (score: 4)
tcttttc CT-rich tract
ttaatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctataagacaggctacatgaatgaacaatctatatatcttactctcttagtatctgcttagtttcttgaaaaactcatccactcgccttaatcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAACTTGATTGGATACTGTGCAGAGAAAGGCCAACACATGCTTATATATGTTTACATGAGTA
- - aagacag
- - - - - - - acatgaa
- - - - - - - - - - - -aacaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catccac