Sequence
atgc intronic sequence ATGC exonic sequence...tctatgcagaattagtgaattgtgattgttgttatttcttctagagcggaaaaaaatactcggatctttactgagctctctcttcatgttgtttctgcagACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCACGGCCCTTGAAAGATGTTATTTTTGTCTCCTATGAGATTATAAACAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G45190.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G45190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 3
tctatgcagaattagtgaattgtgattgt-tgttatttcttctagagcggaaaaaaatactcggatctttactgagctctctcttcatgttg----tttctgcagACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCACGGCCCTTGAAAGATGTTATTTTTGTCTCCTATGAGATTATAAACAAGA
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-gattgcatgatc--ttaattttactcctatgttaagtgttgtcctatagatctg--tacctgtttgaagagagaacttataatttgtactgaccgttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA
upper sequence: AT5G45190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 2
---tctatgcagaattagtgaattgtgattgttgttatttcttctagagcggaaaaaaatactcggatctttactgagctctctcttcatgt-tgtttctgcagACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCACGGCCCTTGAAAGATGTTATTTTTGTCTCCTATGAGATTATAAACAAGA
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ttcctaatttatattaagagaatggtagatgttaaagcat----tataattttaaagattacttaatcaaaatctcataattcacttgatgaacttttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA
upper sequence: AT5G45190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 2
-----tctatgcagaattagtgaattgtgattgttgttatttcttctagagcggaaaaaaatactcggatctttactgagctctctcttcatgttgtttctgcagACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCACGGCCCTTGAAAGATGTTATTTTTGTCTCCTATGAGATTATAAACAAGA
||| |||| | ||| |||| | || || ||| | |||| ||| | || ||| ||| || |||||||||||||||| || || |||||||||||||| |||||||| || ||||| || || | || ||||||||| |||| || |||||||| || ||||||
aggttcctaatttatattaagagaatgtagatgttaaagctg----tatagttttaaagattacttaatcaaaaactcataattcacttgatga-acttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA
upper sequence: AT5G45190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 2
tctatgcagaattagtgaattgtgattgttgttatttcttctagagcggaaaaaaatactcg---gatctttactgagctctctcttcat--gttgtttctgcagACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCACGGCCCTTGAAAGATGTTATTTTTGTCTCCTATGAGATTATAAACAAGA
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----tgcatgggaagaaaagta-gataaaaatgaaatacgcaagagattagttggttttgcatttgatccattcttatcgctaccttctttcatatgctttacagACCATCGCCACAGTATGCATGTTCCTCGCAGGGAAGGTTGAAGAGACTCCACGCCCACTGAAGGATGTTATCCTTGTTTCCTATGAAATAATTCATAAAAMapped 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|152033633|gb|AV832268.2|AV832268EST: TCTGTCATCGATTCTTCTTTCGCCAATCACATGCAAAGAATGACAGAAGG ACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCA
genomic: TCTGTCATCGATTCTTCTTTCGCCAATCACATGCAAAGAATGACAGAAGGgtgagtttat ... gtttctgcagACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCA
EST:
gi|164218279|gb|ES043229.1|ES043229EST: GCCAATCACATGCAAAGAATGACAGAAGG ACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCA
genomic: GCCAATCACATGCAAAGAATGACAGAAGGgtgagtttat ... gtttctgcagACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcggaaaaaaatactcggatctttactgagctctctcttcatgttgtttctgcagACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCACGGCCCTTGAAAGATGTTATTTTTGTCTCCTATGAGATTATAAACAAGA
ctctctcttcatgttg CT-rich tract
aaaaaatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctatgcagaattagtgaattgtgattgttgttatttcttctagagcggaaaaaaatactcggatctttactgagctctctcttcatgttgtttctgcagACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCACGGCCCTTGAAAGATGTTATTTTTGTCTCCTATGAGATTATAAACAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG