Sequence
atgc intronic sequence ATGC exonic sequence...aatggtgtatgtaaagacaaaccaataaaaaaatcaaatcaattatattccttgtacaagaatactgacagatgatgttatatatatgttgtacaaaaagGTCCTCAATGCCAAGCCAGAAAATGTGGAGAGGGAAGCTGAAATTGTAGCACAAAGTGGCCGTTTAGGGGCAGTAACAATTGCCACAAATATGGCAGGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01800.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 3'ss of exon 8
---aatggtgtatgtaaagacaaaccaataaaaaaatcaaatcaattatattccttgtacaagaatactgacagatgatgttatatatatgttgtacaaaaagGTCCTCAATGCCAAGCCAGAAAATGTGGAGAGGGAAGCTGAAATTGTAGCACAAAGTGGCCGTTTAGGGGCAGTAACAATTGCCACAAATATGGCAGGGC
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tctgattatgtgcttcaaactttggaagccacaagctca--tgatttcatttcctaacacatcgaaaatcgtctcaagttttactttgaatttgtactgta-gGTCCTCAATGCTAAACCAGAGAATGTAGAGAGGGAGGCAGAAATTGTAGCTCAGAGTGGACGCCTTGGTGCAGTGACAATTGCCACCAATATGGCGGGAC
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G01060.2 (Glycine max), 3'ss of exon 10
aatggtgtatgtaaagacaaaccaataaaaaaatcaaat----caattatattccttgtacaagaatactgacagatgat-gttatata-tatgttgtacaaaaagGTCCTCAATGCCAAGCCAGAAAATGTGGAGAGGGAAGCTGAAATTGTAGCACAAAGTGGCCGTTTAGGGGCAGTAACAATTGCCACAAATATGGCAGGGC
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---catccatttgaa---agaactataatgaagcttaatcttgcaaccactttttttgtcttaatttttttgggtataaaagtagtgcaatatgtattgtttctagGTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 10
aatggtgtatgtaaagacaaaccaataaaaaaatcaaat---caattatattccttgtacaagaatactgacagatga-tgttatata-tatgttgtacaaaaagGTCCTCAATGCCAAGCCAGAAAATGTGGAGAGGGAAGCTGAAATTGTAGCACAAAGTGGCCGTTTAGGGGCAGTAACAATTGCCACAAATATGGCAGGGC
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-----catccatttgaaagaactataatgaagcttaattttgcaaccactttttttgtcttaatttttttgggtataaatatagtgcaatatgtattgtttctagGTTCTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 10
aatggtgtatgtaaaga-caaaccaataaaaaaatcaaatcaattatattccttgtacaagaatactgacagatgatgttatatatatgttgtacaaaaagGTCCTCAATGCCAAGCCAGAAAATGTGGAGAGGGAAGCTGAAATTGTAGCACAAAGTGGCCGTTTAGGGGCAGTAACAATTGCCACAAATATGGCAGGGC
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-atgctatatttatgtttctcttttgctgccaacatagccaaactactatatctaaatattcgttgtatgagatatattaactaatatcatttaattaaagGTTCTCAATGCGAAACCAGAGAATGTAGAGAGAGAAGCAGAAATTGTTGCACAGAGTGGTCGTCTTGGGGCAGTTACAATTGCTACCAATATGGCAGGTCMapped 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|125289418|gb|EL303503.1|EL303503EST: GAGTGATGAACTATCGCAACTGTTGAGGGAAGCTGGAATAAACTCATGAG GTCCTCAATGCCAAGCCAGAAAATGTGGA
genomic: GAGTGATGAACTATCGCAACTGTTGAGGGAAGCTGGAATAA-CTCATGAGgtaaggcttt ... gtacaaaaagGTCCTCAATGCCAAGCCAGAAAATGTGGA
EST:
gi|124906396|gb|EH980476.1|EH980476EST: CTGGAATAACTCATGAG GTCCTCAATGCCAAGCCAGAAAATGTGGAGAGGGAAGCTGAAATTGTAGCA
genomic: CTGGAATAACTCATGAGgtaaggcttt ... gtacaaaaagGTCCTCAATGCCAAGCCAGAAAATGTGGAGAGGGAAGCTGAAATTGTAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattccttgtacaagaatactgacagatgatgttatatatatgttgtacaaaaagGTCCTCAATGCCAAGCCAGAAAATGTGGAGAGGGAAGCTGAAATTGTAGCACAAAGTGGCCGTTTAGGGGCAGTAACAATTGCCACAAATATGGCAGGGC
tactgac putative branch site (score: 1)
ttatatatatgttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatggtgtatgtaaagacaaaccaataaaaaaatcaaatcaattatattccttgtacaagaatactgacagatgatgttatatatatgttgtacaaaaagGTCCTCAATGCCAAGCCAGAAAATGTGGAGAGGGAAGCTGAAATTGTAGCACAAAGTGGCCGTTTAGGGGCAGTAACAATTGCCACAAATATGGCAGGGC
- - - - - - - - -caaacca
- - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -acaagaa