Sequence
atgc intronic sequence ATGC exonic sequencegtaagttccagctgcatatgtttccttaaagttgaattttttgtctgaagatagactattgcggcagtttggtagatatatcttcttcctctcattggtcccatatgtattctgattgaatacaaatagaaaaactagacttagatgcatgtcacttttgcagATCTGGCGTATAAGGACTGGTGTATGCATACGTCGTTTTGATGCACATTCCCAAGGAGTTACAAGTCTTTCCTTCTCTCGGGATGGAAGCCAATTACTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73720.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 9
gtaagttccagctgcatatgtttccttaaagttgaattttttgtctgaagatagactattgcggcagtttggtagatatatcttcttcctctcattggtcccatatgtattctgattgaatacaaatagaaaaactagacttagatgcatgtcacttttgcagATCTGGCGTATAAGGACTGGTGTATGCATACGTCGTTTTGA---TGCACATTCCCAAGGAGTTACAAGTCTTTCCTTCTCTCGGGATGGAAGCCAATTACTGA
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---------------------------------------------------------gttgtagttgctgacttgctgtttttggaaatgtttat-gttttcacctcaactgttaatatgta-aaacttaaaaactgtatattt-cacatttcatttt---agGTCTGGCGTATTAGGACTGGTCAGTGCTTGCGGCGTCTTGAACGTGCTCATTCTCAAGGTGTCACAAGTGTTTCCTTCTCTCGTGATGGAAGCCAGTTAT---
upper sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G18000.1 (Glycine max), 3'ss of exon 3
gtaagttccagctgcatatgtttccttaaagttgaattttttgtctgaagatagactattgcggcagtttggtagatatatcttcttcctctcattggtcccatatgtattctgattgaatacaaatagaaaaactagacttagatgcatgtcacttttgcagATCTGGCGTATAAGGACTGGTGTATGCATACGTCGTTTTGA---TGCACATTCCCAAGGAGTTACAAGTCTTTCCTTCTCTCGGGATGGAAGCCAATTACTGA
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---------------------------------------------------------gttgtagtttctgacttgctgtttttggaaatttttat-gttttcacctcaactattaatatgtaaaacttaaaaaa-tgtac---aatgcacacttcattt-tagGTCTGGCGTTTTAGGACTAGTCAATGCTTGTGGCGTCTTGAACGTGCTCATTCTCAAGGTGTCACAAGTGTTTCCTTCTCTCGTGATGGAAGCCAGTTAT---
upper sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttccagctgcatatgtttccttaaagttgaattttttgtctgaagatagactattgcggcagtttggtagatatatcttcttcctctcattggtcccatat--gtattctgattgaatacaaatagaaaaactagacttagatgcatgtcacttttg-cagATCTGGCGTATAAGGACTGGTGTATGCATACGTCGTTTTGA---TGCACATTCCCAAGGAGTTACAAGTCTTTCCTTCTCTCGGGATGGAAGCCAATTACTGA
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--------------------------------------------------------tctttcattatactgttggtgaaacattggagt----attgcttcaaaattggaagtttgac---atcaaaattgaagat---gatttatttgcaaactatatgtatcagGTGTGGCGTATAAGGACTGGTCAATGCTTACGCCGACTTGAACGTGCACATTCCCAAGGTGTTACAAGTCTTGTTTTCTCTCGAGATGGAAGTCAGATAC---Mapped 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|125218223|gb|EL232306.1|EL232306EST: GCAGAGATTCAGAGATGCTTGCATCTGGGTCACAAGGTGGAAAGATTAAA ATCTGGCGTATAAGGACTGGTGTATGCATA
genomic: GCAGAGATTCAGAGATGCTTGCATCTGGGTCACAAGATGGAAAGATTAAAgtaagttcca ... acttttgcagATCTGGCGTATAAGGACTGGTGTATGCATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctgattgaatacaaatagaaaaactagacttagatgcatgtcacttttgcagATCTGGCGTATAAGGACTGGTGTATGCATACGTCGTTTTGATGCACATTCCCAAGGAGTTACAAGTCTTTCCTTCTCTCGGGATGGAAGCCAATTACTGA
ttctgat putative branch site (score: 3)
tcactttt putative PPT
aatacaaatagaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttccagctgcatatgtttccttaaagttgaattttttgtctgaagatagactattgcggcagtttggtagatatatcttcttcctctcattggtcccatatgtattctgattgaatacaaatagaaaaactagacttagatgcatgtcacttttgcagATCTGGCGTATAAGGACTGGTGTATGCATACGTCGTTTTGATGCACATTCCCAAGGAGTTACAAGTCTTTCCTTCTCTCGGGATGGAAGCCAATTACTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG