Sequence
atgc intronic sequence ATGC exonic sequencegtattatatcttttatcattcttctctttcaattctcttcttttcattatatatatatatgccttcacagtgcttatctttgtagGTTTATGCTCTCACCAAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79830.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g48620.1 (Oryza sativa), 3'ss of exon 4
-------------gtattatatcttttatcattcttctctttcaattctcttcttttcattatatatatatatgccttcacagtgctt--atctttgtagGTTTATGCTCTCACCAAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATC
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atacaggctaaccacattctttcttggtacctagtgcatctaaaataagattattcttatcgctgatatgttttatatttgcatgcttcaatgtttatagGTGTATGCCTTGACCAAAGAACGGGATACATTAAGGAGAGAGCAAAATAAAAAAAGTGATGCAGCTGCTCTTTTGAAAGAAAAGGATGAAATTATCAGTC
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G168654_T01 (Zea mays), 3'ss of exon 12
------------gtattatatcttttat-cattcttc-tctttcaattctcttcttttcattatatatatatatgccttcacagtgctt--atctttgtagGTTTATGCTCTCACCAAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATC
| || |||||||| ||| ||| ||| | || |||| | | ||| | | | |||| |||| | || | ||||||| ||||| || ||||||||||| |||||||| || ||||||||||| || ||||||||||| || ||||||||||||||||||||||| || || ||||
gtcaaaatgtacaactaatttcttttatgcatgtttcatctatgcatcatcttatgcatagggcata-acttttaccttttttgtgccttgatgtatgtagGTATATGCACTAACCAAAGAGCGTGATACACTAAGGAGAGAACAGAATAAAAAAAGTGATGCAGCTGCCCTTTTGAAAGAAAAGGATGAGATCATCAATC
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G43330.1 (Glycine max), 3'ss of exon 7
---------------gtat-tatatcttttatcat-tcttctctttcaattctcttcttttcattatatatatatatgccttcacagtgcttatctttgtagGTTTATGCTCTCACCAAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATC
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gaagattattaggcattatgtatatgttttgaagtgtatgctacctcatttgagctacagctgttatgggattttatgtgtttttggtgtttaa--ttgcagGTTTATGCTCTCACTAAGGAAAGGGATACACTCCGCCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATC
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G01980.1 (Glycine max), 3'ss of exon 5
---------------gtattatatcttttatcattcttctctttcaattctcttcttt--tcattatatatatatatgccttcacagtgcttatctttgtagGTTTATGCTCTCACCAAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATC
| | | || |||| ||| | ||| || || | |||| | |||| || ||| ||| ||| |||||||||||||||| || || |||||||||| | |||| ||||| || ||||||||||| || || || ||||||||||||||||||||||| ||||
tgtgtctttcttttgaggatgaagatcaaatttctcttttctcttaatactgagctataactgttatgggattttatgtgtttttggtgtttaa--ttgcagGTTTATGCTCTCACTAAGGAAAGGGATACACTCCGTCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATC
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 4
--------------gtattatatcttttatcattcttctct-ttcaattctcttc-ttttcattatatatatatatgccttcacagtgcttatctttgtagGTTTATGCTCTCACCAAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATC
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ccttgataagatattaattaaaaaactcaaaatttatctttgtttaattgttaggattcttgttggtcttgtataaatgcatccggtctgtatgttt-cagGTATATGCCCTTACTAAGGAAAGGGATACACTACGAAGAGAACATAGCAGAAAAAGTGATGCTGCTGCCCTTTTGAAAGAAAAAGATGAAATAATCAACCMapped 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|125213581|gb|EL228395.1|EL228395EST: AGTCTTTGCGAGAAGAATACCATCAGAGAGTTGCAACTCTTGAGAGGAAG GTTTATGCTCTCACC
genomic: AGTCTTTGCGAGAAGAATACCATCAGAGAGTTGCAACTCTTGAGAGGAAGgtattatatc ... atctttgtagGTTTATGCTCTCACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattctcttcttttcattatatatatatatgccttcacagtgcttatctttgtagGTTTATGCTCTCACCAAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATC
cttatcttt CT-rich tract
tcttcttttcattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattatatcttttatcattcttctctttcaattctcttcttttcattatatatatatatgccttcacagtgcttatctttgtagGTTTATGCTCTCACCAAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG