Sequence
atgc intronic sequence ATGC exonic sequencegtgtgttttctcttcttttttctaattttttaatcaccctaggtgcaatcactaaatgcagaatttacatgtagCAAGAGCCCAATTAACCAAGCAACTTCTAAAGCAATGCTGACTCAGATGATAAGCATTGTATTCAGGAGAATGGAGACTGACATT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G43300.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G43300.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 5
-------gtgtgtt-ttctcttcttttttctaatttttta----atcaccctaggtgcaat---cactaaatgcagaatttacat----gtagCAAGAGCCCAATTAACCAAGCAACTTCTAAAGCAATGCTGACTCAGATGATAAGCATTGTATTCAGGAGAATGGAGACTGA-CATT
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gtacctgttatatcactaccttcttgtttgcagtatgttgccttgttgccctttggaccatgtatgataatttattcatttgtattttgttagCAAGAGCCCTGTGAACCAGGCTACCTCAAAGGCTATGTTAACCCAGATGATCAGCATTGTATTCAGGAGAATGGAATCTGAGCAG-
upper sequence: AT3G43300.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 6
----gtgtgttttctcttcttttttctaattttttaatcaccctaggtgcaatcactaaatgcagaattt---acatgtagCAAGAGCCCAATTAACCAAGCAACTTCTAAAGCAATGCTGACTCAGATGATAAGCATTGTATTCAGGAGAATGGAGACTGACATT
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gtattaatcatttctattctgtcttcaagtgttgttattgtta-atctataatactgagattcattgttttggatttgtagCAAGAGTCCTATAAACCAAGCAACGTCAAAGGCAATGCTGACACAGATGATCAGCATCACTTTCAGGAGAATGGAAACTGATCCG
upper sequence: AT3G43300.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 6
----gtgtgttttctcttcttttttctaattttttaatcaccctaggtgcaatcactaaatgcagaattt----acatgtagCAAGAGCCCAATTAACCAAGCAACTTCTAAAGCAATGCTGACTCAGATGATAAGCATTGTATTCAGGAGAATGGAGACTGACATT
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gtatcaatcatttctattctgtcttcaagagctgttattgtta-atctataatactgagatttattgtttttggatttgtagCAAGAGTCCTATAAACCAAGCAACGTCGAAGGCAATGTTGACACAGATGATCAGCATCACTTTCAGGAGAATGGAAACTGATCCA
upper sequence: AT3G43300.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 7
gtgtgttttctcttcttttttc--taattttttaat--caccctaggtgcaatcactaaatgcagaattt--acatgtagCAAGAGCCCAATTAACCAAGCAACTTCTAAAGCAATGCTGACTCAGATGATAAGCATTGTATTCAGGAGAATGGAGACTGACATT
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gttctttatttacctttatctcaatggctgcatgatagcaacttgaactagaactcatgatttatagtttgaatatgtagCAAAAGTCCTATAAACCAAGCAACATCAAAGGCAATGTTGACCCAGATGATTAGCATCATATTCAGAAGGATGGAAACTGATCCGMapped 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|125280105|gb|EL294190.1|EL294190EST: GAGTTATTAGAGTTTGCTATAACATTGCTCTAAACAG CAAGAGCCCAATTAACCAAGCAACTTCTAAAGCAATGCTGACT
genomic: GAGTTATTAGAGTTTGCTATAACATTGCTCTAAACAGgtgtgttttc ... ttacatgtagCAAGAGCCCAATTAACCAAGCAACTTCTAAAGCAATGCTGACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctaattttttaatcaccctaggtgcaatcactaaatgcagaatttacatgtagCAAGAGCCCAATTAACCAAGCAACTTCTAAAGCAATGCTGACTCAGATGATAAGCATTGTATTCAGGAGAATGGAGACTGACATT
cactaaa putative branch site (score: 2)
attttttaatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgttttctcttcttttttctaattttttaatcaccctaggtgcaatcactaaatgcagaatttacatgtagCAAGAGCCCAATTAACCAAGCAACTTCTAAAGCAATGCTGACTCAGATGATAAGCATTGTATTCAGGAGAATGGAGACTGACATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA