Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcctaaacatgtaaaataaacacagtaattggcaaatgtttatatatttggtaatgatgataaatctgtaaaaaaaaaatggaacagGTTCAAGATGTTCAATATGCAGTTTGATGAGTTGCATCAGAGACAATCGCAATGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03540.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G33590.1 (Glycine max), 3'ss of exon 10
gtaagtcctaaacatgtaaaataaacacagtaat-tggcaaatgtttatatatttggtaatgatgataaatctgtaaaaaaaaaatggaacagGTTCAAGATGTTCAATATGCAGTTTGATGAGTTGCATCAGAGACAATCGCAATGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTT
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gtagcctttcagttgcttttttatgggcttttgtctgggagagtaacttttttttacttcttttgacatgtctatgtgtattgtgttgt-cagGTTTAAGGCATTCAATATTATGTTTGAGGAACTCCATCAGAAACAATCGCAATGGACAGTTCCAGACTCCGAGTTGCGAGAATCTCTTAGGCTAGCAGTT
upper sequence: AT5G03540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G34000.1 (Glycine max), 3'ss of exon 10
gtaagtcctaaa---catgtaaaataaacacagtaattggcaaatgtttatatatttggtaatgatgataaatctgtaaaaaaaaaatggaacagGTTCAAGATGTTCAATATGCAGTTTGATGAGTTGCATCAGAGACAATCGCAATGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTT
||| | | | | | | | | || | | || | | | | | | | | ||| | | | | |||||| ||| |||||||| |||||| || | ||||||| |||||| |||||||||||||| ||||| ||||| ||||||| || || ||||| |||
gtagcctttcagttgcttttttatggagttttttgtttagggagagtattt-tctgcacttcttttcacgcatcaatgtgtattgtgttgt-cagGTTTAAGTCATTCAATATTATGTTTGAGGAACTCCATCAGAAACAATCTCAATGGACAGTTCCTGACACTGAGTTGCGAGAGTCTCTTAGGCTTGCAGTT
upper sequence: AT5G03540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 10
----------------gtaagtcctaaacatgtaaaataaacacagtaattggcaaatgtttatatatttggtaatgatgataaatctgtaaaaaaaaaatggaa------cagGTTCAAGATGTTCAATATGCAGTTTGATGAGTTGCATCAGAGACAATCGCAATGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTT
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gttatgattaagttgcatccttcttatagat-tgctttccttcttttctttaaataatatgtaatcttcttataaatattttaacctggctggagaagtgccttttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTTMapped 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|125262063|gb|EL276148.1|EL276148EST: CAGTGGAGTTTCAAGAGGATTATTAAAAGAGAG GTTCAAGATGTTCAATATGCAGTTTGATGAGTTGCATCAGAGACAATCGCA
genomic: CAGTGGAGTTTCAAGAGGATTATTAAAAGAGAGgtaagtccta ... aatggaacagGTTCAAGATGTTCAATATGCAGTTTGATGAGTTGCATCAGAGACAATCGCA
EST:
gi|124752166|gb|EH842296.1|EH842296EST: TTAGAGGGAGGAAACAGCAGTGGAGTTTCAAGAGGATTATTAAAAGAGAG GTTCAAGATGTTCAATATGCAGTTTGA
genomic: TTAGAGGGAGGAAACAGCAGTGGAGTTTCAAGAGGATTATTAAAAGAGAGgtaagtccta ... aatggaacagGTTCAAGATGTTCAATATGCAGTTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaatgtttatatatttggtaatgatgataaatctgtaaaaaaaaaatggaacagGTTCAAGATGTTCAATATGCAGTTTGATGAGTTGCATCAGAGACAATCGCAATGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTT
taatgatgataaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcctaaacatgtaaaataaacacagtaattggcaaatgtttatatatttggtaatgatgataaatctgtaaaaaaaaaatggaacagGTTCAAGATGTTCAATATGCAGTTTGATGAGTTGCATCAGAGACAATCGCAATGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT