Sequence
atgc intronic sequence ATGC exonic sequencegtgagtccattcacattatgtcgttttcatgtaatgaaaataccttattaggcttagggtttcccaaattaggtggttagtcttttttcataaaggaaataaaaaatatgccaagtttatgttttgtgtgatgattatgatcagAGATGGACCGGAGCGTGAAACGGATGGTGAAGTTGATAGAGGAGGATGCAGATTCTTTTGCTAAGAAGGCAGAGATGTATTACCAGTCAAGACCTGAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G58320.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G58320.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G38570.1 (Glycine max), 3'ss of exon 2
gtgagtccattcacattatgtcgttttcatgtaatgaaaataccttattaggcttagggtttcccaaattaggtggttagtcttttttcataaaggaaataaaaaatatgccaagtttatgttttgtgtgatgattatgatcagAGATGGACCGGAGCGTGAAACGGATGGTGAAGTTGATAGAGGAGGATGCAGATTCTTTTGCTAAGAAGGCAGAGATGTATTACCAGTCAAGACCTGAGCT
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-------------------------tttttggggtggagggag------ggggtttgcatcttgctttgtatatg-tcaatccttttttgt--------cataatgtcgtccaagaaaatg----acatgattttcattctcagAGATGGACCGGAGTGTGAAGCGAATGTTGAAGCTGATAGAAGAGGATGCAGATTCATTTGCCAAAAAAGCTGAAATGTATTATCAGAAGAGGCCAGAATT
upper sequence: AT5G58320.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G40300.1 (Glycine max), 3'ss of exon 2
gtgagtccattcacattatgtcgttttcatgtaatgaaaataccttattaggcttagggtttcccaaattaggtggttagtcttttttcataaaggaaataaaaaatatgccaagtttatgttttgtgtgatgattatgatcagAGATGGACCGGAGCGTGAAACGGATGGTGAAGTTGATAGAGGAGGATGCAGATTCTTTTGCTAAGAAGGCAGAGATGTATTACCAGTCAAGACCTGAGCT
||| | || | || || || | | | | || || | | |||||| | | | || ||||| ||| ||| || | || ||||||||||||||||| ||||| || ||| ||||| ||||||| |||||||||||||| ||||| || || || || |||||||| ||| || || || |
------------------------tttttcggggtggaggtag------ggggtttgcatcttactctgtatatg-tcaatcttttat---------atcataatgccgtccaagaaaatgacttg----attttcattctcagAGATGGACCGGAGTGTGAAGCGAATGTTGAAGCTGATAGAAGAGGATGCAGATTCATTTGCCAAAAAAGCTGAAATGTATTATCAGAAGAGGCCAGAATT
upper sequence: AT5G58320.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g08170.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtccattcacattatgtcgttttcatgtaatgaaaataccttattaggcttagggtttcccaaattaggtggttagtcttttttcataaaggaaataaaaaatatgccaagtttatgttttgtgtgatgattatgatcagAGATGGACCGGAGCGTGAAACGGATGGTGAAGTTGATAGAGGAGGATGCAGATTCTTTTGCTAAGAAGGCAGAGATGTATTACCAGTCAAGACCTGAGCT
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--------------------ttgtctcattgttgagacaaaataatgttttgccaa---ttaccctgtgtaaattttaaaacagtttttgaatagaaactgataaaag---------------------ggtacttggcctcagAGATGGACCAGAGTGTGAAACGGATGTTGAAGCTGATTGAAGAGGATGGGGATTCATTTGCAAAAAAGGCTGAGATGTATTATCAGAAGAGACCTGAATTMapped 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|86072850|gb|DR368607.1|DR368607EST: TAGTCATATCGGTCTCAAAAATTCTAAGTGGCTTGAGAATAATCTCGATG AGATGGACCGGAGCGTGAAACGGATGGTGAAGTTGATAGAGGAGGATGCAG
genomic: TAGTCATATCGGTCTCAAAAATTCTAAGTGGCTTGAGAATAATCTCGATGgtgagtccat ... ttatgatcagAGATGGACCGGAGCGTGAAACGGATGGTGAAGTTGATAGAGGAGGATGCAG
EST:
gi|19874799|gb|AU235630.1|AU235630EST: TAGTCATATCGGTCTCAAAAATTCTAAGTGGCTTGAGAATAATCTCGATG AGATGGACCGGAGCGTGAAACGGATGGTGAAGTTGATAGAGGAGGATGCAG
genomic: TAGTCATATCGGTCTCAAAAATTCTAAGTGGCTTGAGAATAATCTCGATGgtgagtccat ... ttatgatcagAGATGGACCGGAGCGTGAAACGGATGGTGAAGTTGATAGAGGAGGATGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaaggaaataaaaaatatgccaagtttatgttttgtgtgatgattatgatcagAGATGGACCGGAGCGTGAAACGGATGGTGAAGTTGATAGAGGAGGATGCAGATTCTTTTGCTAAGAAGGCAGAGATGTATTACCAGTCAAGACCTGAGCT
aaataaaaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtccattcacattatgtcgttttcatgtaatgaaaataccttattaggcttagggtttcccaaattaggtggttagtcttttttcataaaggaaataaaaaatatgccaagtttatgttttgtgtgatgattatgatcagAGATGGACCGGAGCGTGAAACGGATGGTGAAGTTGATAGAGGAGGATGCAGATTCTTTTGCTAAGAAGGCAGAGATGTATTACCAGTCAAGACCTGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG