Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtgtctggctccttgtcttaaataattatgttttggtccttaacatctgtgtaccaagcttctttataacgtatcaatatgccacactgttggtttgttcagtatgtttgtttgactataataacatagatcccaatttctggatatttctctatatcacgtgaataatgtcagtgtacttgttatgcagGAACCAATGGTCAATACGTATGCTAACTTTAGAGATGATGTTCTTCCCCGCATCAAAAAGCTTGGATATAATGCTGTTCAAATTATGGCCATACAAGAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03650.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 9
gtgtgtgtctggctccttgtcttaaataattatgttttggtccttaacatctgtgtaccaagcttctttataacgtatcaatatgccacactgttggtttgttcagtatgtttgtttgactataataacatagatcccaatttctggatatttctctatatcacg-tgaataatgtcagtgtacttgttatg--cagGAACCAATGGTCAATACGTATGCTAACTTTAGAGATGATGTTCTTCCCCGCATCAAAAAGCTTGGATATAATGCTGTTCAAATTATGGCCATACAAGAAC
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--------------------------------------------------------------------------------------catgcctaccatttgtata-catttttttttgggcgt-------ctgttggtaatttatg---attttcctgtactatgctggctggtattaattttaatattgcaatcagGAGCCAAAGATCAACACGTATGCAAACTTTAGGGATGAGGTGCTTCCAAGAATCAAAAAGCTTGGATACAATGCAGTGCAAATAATGGCAATTCAAGAGC
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 9
gtgtgtgtctggctccttgtcttaaataattatgttttggtccttaacatctgtgtaccaagcttctttataacgtatcaatatgccacactgttggtttgttcagtatgtttgtttgactataataacatagatcccaatttctggatatttctctatatcacgtgaataatgtcagtgtacttgttatgcagGAACCAATGGTCAATACGTATGCTAACTTTAGAGATGATGTTCTTCCCCGCATCAAAAAGCTTGGATATAATGCTGTTCAAATTATGGCCATACAAGAAC
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-----------------------------------------------------------------------------tatatgtaccattctattgggtaattgaa-------gtttcagtactataaactatgatc--atct----atacttc---agataaactgagtattttaggtg-atctgttacacagGAACCAAAGATAAATACATATGCTAACTTCAGAGATGAGGTGCTTCCAAGAATTAAAAAGCTTGGATACAATGCAGTACAGATAATGGCAATCCAGGAAC
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA19G37750.1 (Glycine max), 3'ss of exon 9
gtgtgtgtctggctccttgtcttaaataattatgttttggtccttaacatctgtgtaccaagcttctttataacgtatcaatatgccacactgttggtttgttcagtatgtttgtttgactataataacatagatcccaatttctgg--atatttctctatatcacgtgaataatgtcagtgtacttgttatgcagGAACCAATGGTCAATACGTATGCTAACTTTAGAGATGATGTTCTTCCCCGCATCAAAAAGCTTGGATATAATGCTGTTCAAATTATGGCCATACAAGAAC
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------------------------------------------------------------------------------------------------ttttgtattagagattaaatctatgatgttcaagaaagttcctatgtatagtatcagttctttttctactattaacaattttgtgaaccatgcggcgcagGAGCCAAAAATCAATACATATGTCAATTTTAGAGATGATGTACTGCCTCGCATTAAAAGGCTTGGCTATAATGCTGTCCAGATTATGGCTATCCAAGAAC
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 9
gtgtgtgtctggctccttgtcttaaataattatgttttggtccttaacatctgtgtaccaagcttctttataacgtatcaatatgccacactgttggtttgttcagtatgtttgtttgactataataacatagatcccaatttctggatatttctctatatcacgtgaataatgtcagtgtacttgttatgcagGAACCAATGGTCAATACGTATGCTAACTTTAGAGATGATGTTCTTCCCCGCATCAAAAAGCTTGGATATAATGCTGTTCAAATTATGGCCATACAAGAAC
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--------------------------------------------------------------------------------------------attggaaaaatttaaatatccaccctacccctcatccttatgctttcaattatgcatagaattttttaatactc--attttactgttgactttgagatgtagGAGCCAGTAGTCAACACATATGCCAACTTTAGAGATGATGTGCTACCTCGCATCAAAAGGCTTGGTTATAATGCTGTCCAGATAATGGCAATTCAGGAGCMapped 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|125137096|gb|EL177054.1|EL177054EST: GACCTAAGTCGCTAAGGATTTATGAAGCACATGTTGGCATGAGTAGCACG GAACCAATGGTCAATACGTATGCTAACTTTAGAG
genomic: GACCTAAGTCGCTAAGGATTTATGAAGCACATGTTGGCATGAGTAGCACGgtgtgtgtct ... tgttatgcagGAACCAATGGTCAATACGTATGCTAACTTTAGAG
EST:
gi|125270966|gb|EL285051.1|EL285051EST: GAAGCACATGTTGGCATGAGTAGCACG GAACCAATGGTCAATACGTATGCTAACTTTAGAGATGATGTTCTTCCCCGC
genomic: GAAGCACATGTTGGCATGAGTAGCACGgtgtgtgtct ... tgttatgcagGAACCAATGGTCAATACGTATGCTAACTTTAGAGATGATGTTCTTCCCCGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttctggatatttctctatatcacgtgaataatgtcagtgtacttgttatgcagGAACCAATGGTCAATACGTATGCTAACTTTAGAGATGATGTTCTTCCCCGCATCAAAAAGCTTGGATATAATGCTGTTCAAATTATGGCCATACAAGAAC
atatttctctatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtgtctggctccttgtcttaaataattatgttttggtccttaacatctgtgtaccaagcttctttataacgtatcaatatgccacactgttggtttgttcagtatgtttgtttgactataataacatagatcccaatttctggatatttctctatatcacgtgaataatgtcagtgtacttgttatgcagGAACCAATGGTCAATACGTATGCTAACTTTAGAGATGATGTTCTTCCCCGCATCAAAAAGCTTGGATATAATGCTGTTCAAATTATGGCCATACAAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC