Sequence
atgc intronic sequence ATGC exonic sequence...ttgttattttcattgatcattcattatggagtctagtctctaatctctgaagattcaaatatcagaatacattctctaatctgttttaaaaattcaccagGAGGCCAGATTACTGCCTTGGACCTCATTTACGACAAATGCTGATTTACGGTTGCACCCGGCTAGAGATAGGTGTCCAGAGCACATATGAAGATGTTGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50320.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 3
-----------------------ttgttattttcattgatc--attcattatgga-gtctagtct---ctaatctctgaagattcaaatatcagaatacattctctaatctgttttaaaaattcaccagGAGGCCAGATTACTGCCTTGGACCTCATTTACGACAAATGCTGATTTACGGTTGCACCCGGCTAGAGATAGGTGTCCAGAGCACATATGAAGATGTTGCC
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gtaagtatcatcgcataattggatggtgcttcttattacttcaattcaaaaggaatgtgttgcctttcccacttccctatgaatttaatccca--atgaaatgttt--ttttctctcggaattc--tagGAGACCTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTATGGTTGTACTCGCCTGGAAATTGGTGTCCAGAGTACATATGAAGATGTTGCC
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G18150.1 (Glycine max), 3'ss of exon 3
ttgttattttcattgatcattcattatggagtcta---gtctctaatctctgaagattcaaatatcagaatacattctctaatc---tgttttaaaaattcaccagGAGGCCAGATTACTGCCTTGGACCTCATTTACGACAAATGCTGATTTACGGTTGCACCCGGCTAGAGATAGGTGTCCAGAGCACATATGAAGATGTTGCC
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------gatttagtgaaaacgttctgggaaatttacatggcaatagtgtggtgtaacacatctatgatgagcttttatcaaattctgcactttttaaatttaacagGAGGCCAGATTATTGTCTTGGGCCTCACTTGCGCCAAATGCTTTCTTATGGTTGTACACGATTGGAGATTGGAGTCCAAAGCACCTATGAAGATGTTGCT
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 3'ss of exon 3
-ttgttattttcattgatcat-tcattatggagtctagtctctaatctctgaagattcaaatatcagaatacattctctaatctgttttaaaaattcaccagGAGGCCAGATTACTGCCTTGGACCTCATTTACGACAAATGCTGATTTACGGTTGCACCCGGCTAGAGATAGGTGTCCAGAGCACATATGAAGATGTTGCC
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atcattgtaattgaagaccatgtcattttgcaagttagtggtatctccttccactgacacatattatttaatatattcttgtccttttttaa--tctatcagGAGGCCAGATTACTGTCTTGGACCTCATTTGCGGCAAATGCTTTCTTATGGTTGTACACGGCTGGAGATTGGAGTTCAAAGCACCTACGAGGATGTTGCCMapped 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|125030326|gb|EL102595.1|EL102595EST: GCTTACTCTGAACATAGTGCAACTAAATGCATTGGGATGACAATTGAAAC GAGGCCAGATTACTGCCTTGGACCTCA
genomic: GCTTACTCTGAACATAGTGCAACTAAATGCATTGGGATGACAATTGAAACgtgagttcga ... aattcaccagGAGGCCAGATTACTGCCTTGGACCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgaagattcaaatatcagaatacattctctaatctgttttaaaaattcaccagGAGGCCAGATTACTGCCTTGGACCTCATTTACGACAAATGCTGATTTACGGTTGCACCCGGCTAGAGATAGGTGTCCAGAGCACATATGAAGATGTTGCC
ctctaat putative branch site (score: 3)
taatctgttttaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttattttcattgatcattcattatggagtctagtctctaatctctgaagattcaaatatcagaatacattctctaatctgttttaaaaattcaccagGAGGCCAGATTACTGCCTTGGACCTCATTTACGACAAATGCTGATTTACGGTTGCACCCGGCTAGAGATAGGTGTCCAGAGCACATATGAAGATGTTGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - atctctg
- - - - - - - - - - - - - - - - - - - - - - - - - - attcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcagaa