Sequence
atgc intronic sequence ATGC exonic sequencegcaagttatccatcttatcctatcttcttctccttctgtgacctaactagtttcgatattttaaaaagtatgggaacaggtcaatgattaaccgtaaaacagctttatataacttcaattgtcatattttttcagGAGCTCATATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTGTCATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G20290.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 9
gcaagttatccatcttatcctatcttcttctccttctgtgacctaactagtttcgatattttaaaaagtatgggaacaggtcaatgattaaccgtaaaacagctttatataacttcaattgtcatattttttcagGAGCTCATATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTGTCATG
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-------gtaaacaggatgaaatattgtgttccttttccttcttattgagaatt-atattttccattctctttctacacatt-----ttcccttgaaaaaaatgtaacaatatctgagttgt--ttctcttgcagGTGCTCATATTGGTCCAGAGCCTACAACTGACAGATTTGTTGTTATTACT
upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 9
gcaagttatccatcttatcctatcttcttctccttctgtgacctaactagtttcgatattttaaaaagtatgggaacaggtcaatgattaaccgtaaaacagctttatataacttcaattgtcatattttttcagGAGCTCATATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTGTCATG
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-------------------------------atatatacacacacacacacacacatacatgggggattgttcacacttattatgaaatgtatgttattgaattttttctaattctaatga----atgtcactagGAGCTCATATTGGACCAGAGCCAACAACTGATAGGTTTGTTGTTGTCATG
upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G46350.2 (Glycine max), 3'ss of exon 9
------------------------------------------------------------------gcaagttatcc-atcttatcctatcttcttctccttctgtgacctaactagtttcgatattttaaaaagtatgggaacaggtcaatgattaaccgtaaaacagctttatataacttcaattgtcatattttttcagGAGCTCATATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTGTCATG
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gcacgtgattctcctttctctatatccatatatgtatatgtcacattgcttatatctgatttatgaagaaataattttaaatgcatttatttattttatttaatattctttgtaaaattgtaggatgattaataggatgatataacat-atttttaaaatgttattaatctttgtcttgtttttcccataa-atgttgatagGAGCACATATTGGACCTGAGCCAACAACTGATAGGTTTGTTGTTGTCATGMapped 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|125133618|gb|EL174993.1|EL174993EST: TTAAGCATTTGCTTAAATCTACTTATCCAG GAGCTCATATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTG
genomic: TTAAGCATTTGCTTAAATCTACTTATCCAGgcaagttatc ... attttttcagGAGCTCATATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTG
EST:
gi|125301204|gb|EL315289.1|EL315289EST: CACAGGAAAAACAACATTCATTAAGCATTTGCTTAAATCTACTTATCCAG GAGCTCATATTGGACCAGAGC
genomic: CACAGGAAAAACAACATTCATTAAGCATTTGCTTAAATCTACTTATCCAGgcaagttatc ... attttttcagGAGCTCATATTGGACCAGAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaatgattaaccgtaaaacagctttatataacttcaattgtcatattttttcagGAGCTCATATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTGTCATG
tattttttc CT-rich tract
tttatataacttcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagttatccatcttatcctatcttcttctccttctgtgacctaactagtttcgatattttaaaaagtatgggaacaggtcaatgattaaccgtaaaacagctttatataacttcaattgtcatattttttcagGAGCTCATATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTGTCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA